user22057: Context
This relates to a 
post including the compound FADH2, in a sentence within the main text (technically ‘in-line’), set as I have here, using HTML ‘sub’ markup to render the subscript, and thus in the same default sans-serif typeface as the rest of the text. I noticed that someone had edited this using LaTeX so that it was rendered in a larger size, in italic (since removed), and in a serif face (i.e. visually different from the rest of the text): $\ce{FADH2}$. I felt that this was not only unnecessary, but inferior to the original, and so reverted it, commenting on the fact that I had done so and the reason why. The person who had made the edit replied with the statement:

“LaTeX has been the preferred mode for both Mathematical as well as Chemical equations/formulae on SE; and its italic by default.”

The purpose of this post is both to question this assertion and suggest  recommendations for users wishing to sub- super-script in chemical formulae.
Proposal

Ideally SE would be asked to provide an edit option to set subscript and superscript within text, as for word processors rendering it through the HTML sub and sup tags. However the version of Markdown used by SE does not support this, and I imagine the request has been made before. Hence it seems unlikely that they will agree.
Thus, in the absence of support in Markdown I propose the following guidelines for SE Biology users.
(i) For in-text chemical formulae either HTML tags or LaTeX may be used.
(ii) HTML tags are preferred as they do not change the typeface, producing the most standard apparance. [An explanation of the two tags would follow].
(iii) For chemical equations LaTeX is appropriate, although graphics of equations obtained using GUI-based methods are also acceptable.

Technique for achieving subscripts and superscripts: Current Policy
Contrary to what I have quoted above, the reference to LaTeX in the SE Biology Advanced Editing Help is:

LaTeX
  Biology Stack Exchange uses MathJax to render LaTeX. You can use
  single dollar signs to delimit inline equations, and double dollars
  for blocks

That’s it. Nothing about being the preferred mode for anything, and reference solely to equations.
As far as HTML goes:

Inline HTML
  If you need to do something that Markdown can't handle,
  use HTML.

Note the reference to Inline HTML.
Desired appearance of in-line chemical formulae: Policy of Chemical publications
Clearly, if SE allows you to achieve an effect by two alternative methods, the key to which is preferable is the effect they produce. That is what is important to the reader.
The arbiter of this is surely printed publications — both books and journals — in the area of chemistry and biological chemistry, and their on-line versions 
The universal agreement for in-line chemical formulae (not equations) is to render them in the same typeface as the rest of the text. Examples shown below are from The Journal of the American Chemical Society and the text book Biochemistry, by Berg et al.. (The text here is in a serif face, as is normal in printed publications. The point is it is in exactly the same style as the rest of the text.)


And the reason publications follow this convention is easy to see. If you set something in the text in a different face or weight or style you are drawing attention to it. Drosophila melanogaster is in italics because it is Latin species name. In other cases italics or bold are used for emphasis or perhaps to indicate something is a specific technical name rather than its normal English meaning. Although it is not customary to set chemical equations in a different typeface, one might justify that by saying that it helps them stand out from the surrounding text, like an illustration. 
Can LaTeX be tamed?
I notice since my comment that the answer to the question using LaTeX for chemical names has had the italics removed. I do not use LaTeX myself, so I do not know if it is also possible to have the compounds rendered in the default face. I somehow doubt it, because that presumably goes against the mathematical conventions that LaTeX was designed to follow. However if it is possible, perhaps it can be explained to users. 
Otherwise, anyone who can follow the arcane markup of LaTeX (dollar, backslash, ce, curly bracket, text, close bracket, dollar) can surely manage sub and sup HTML tags. One suspects that it is ‘religious’ thing. If so, I doubt whether it will find many converts among contemporary biologists.

user3624: I agree, and dont think that LaTeX-use should be "mandatory". I like and often use LaTeX for equation, but one additional problem, besides the formatting you mentioned, is that it is often rendered incorrectly on mobile devices . For instance, in the answer to the Q you link to I see this (Xperia/Chrome):


22057: <p><strong>Context</strong></p>

<p>This relates to a 
<a href="https://biology.stackexchange.com/questions/10313/why-is-fad-rather-than-nad-reduced-in-the-succinate-dehydrogenase-reaction-of?noredirect=1#comment131904_10313">post</a> including the compound FADH<sub>2</sub>, in a sentence within the main text (technically ‘in-line’), set as I have here, using HTML ‘sub’ markup to render the subscript, and thus in the same default sans-serif typeface as the rest of the text. I noticed that someone had edited this using LaTeX so that it was rendered in a larger size, in italic (since removed), and in a serif face (i.e. visually different from the rest of the text): $\ce{FADH2}$. I felt that this was not only unnecessary, but inferior to the original, and so reverted it, commenting on the fact that I had done so and the reason why. The person who had made the edit replied with the statement:</p>

<blockquote>
  <p>“LaTeX has been the preferred mode for both Mathematical as well as Chemical equations/formulae on SE; and its italic by default.”</p>
</blockquote>

<p>The purpose of this post is both to question this assertion and suggest  recommendations for users wishing to sub- super-script in chemical formulae.</p>

<p><strong>Proposal</strong></p>

<ol>
<li><p>Ideally SE would be asked to provide an edit option to set subscript and superscript within text, as for word processors rendering it through the HTML sub and sup tags. However the version of <em>Markdown</em> used by SE does not support this, and I imagine the request has been made before. Hence it seems unlikely that they will agree.</p></li>
<li><p>Thus, in the absence of support in <em>Markdown</em> I propose the following guidelines for SE Biology users.<br>
(i) For in-text chemical formulae either HTML tags or LaTeX may be used.<br>
(ii) HTML tags are preferred as they do not change the typeface, producing the most standard apparance. [An explanation of the two tags would follow].<br>
(iii) For chemical equations LaTeX is appropriate, although graphics of equations obtained using GUI-based methods are also acceptable.</p></li>
</ol>

<p><strong>Technique for achieving subscripts and superscripts: Current Policy</strong></p>

<p>Contrary to what I have quoted above, the reference to LaTeX in the <a href="https://biology.stackexchange.com/editing-help">SE Biology Advanced Editing Help</a> is:</p>

<blockquote>
  <p><strong>LaTeX</strong><br>
  Biology Stack Exchange uses MathJax to render LaTeX. You can use
  single dollar signs to delimit inline equations, and double dollars
  for blocks</p>
</blockquote>

<p>That’s it. Nothing about being the preferred mode for anything, and reference solely to equations.</p>

<p>As far as HTML goes:</p>

<blockquote>
  <p><strong>Inline HTML</strong><br>
  If you need to do something that Markdown can't handle,
  use HTML.</p>
</blockquote>

<p>Note the reference to Inline HTML.</p>

<p><strong>Desired appearance of in-line chemical formulae: Policy of Chemical publications</strong></p>

<p>Clearly, if SE allows you to achieve an effect by two alternative methods, the key to which is preferable is the effect they produce. <em>That</em> is what is important to the <em>reader</em>.</p>

<p>The arbiter of this is surely printed publications — both books and journals — in the area of chemistry and biological chemistry, and their on-line versions </p>

<p>The universal agreement for in-line chemical formulae (not equations) is to render them in the <em>same typeface as the rest of the text</em>. Examples shown below are from <a href="https://pubs.acs.org/doi/pdf/10.1021/ja806467a" rel="nofollow noreferrer">The Journal of the American Chemical Society</a> and the text book <a href="https://www.ncbi.nlm.nih.gov/books/NBK22352/#A2498" rel="nofollow noreferrer"><em>Biochemistry</em>, by Berg <em>et al.</em></a>. (The text here is in a serif face, as is normal in printed publications. The point is it is in exactly the same style as the rest of the text.)</p>

<p><a href="https://i.stack.imgur.com/bwtqM.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/bwtqM.png" alt="JACS example of chemical formulae face"></a></p>

<p><a href="https://i.stack.imgur.com/Kf6VY.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Kf6VY.png" alt="Berg et al. example of chemical formulae face"></a></p>

<p>And the reason publications follow this convention is easy to see. If you set something in the text in a different face or weight or style you are drawing attention to it. <em>Drosophila melanogaster</em> is in italics because it is Latin species name. In other cases italics or bold are used for emphasis or perhaps to indicate something is a specific technical name rather than its normal English meaning. Although it is not customary to set chemical equations in a different typeface, one might justify that by saying that it helps them stand out from the surrounding text, like an illustration. </p>

<p><strong>Can LaTeX be tamed?</strong></p>

<p>I notice since my comment that the answer to the question using LaTeX for chemical names has had the italics removed. I do not use LaTeX myself, so I do not know if it is also possible to have the compounds rendered in the default face. I somehow doubt it, because that presumably goes against the mathematical conventions that LaTeX was designed to follow. However if it is possible, perhaps it can be explained to users. </p>

<p>Otherwise, anyone who can follow the arcane markup of LaTeX (dollar, backslash, ce, curly bracket, text, close bracket, dollar) can surely manage sub and sup HTML tags. One suspects that it is ‘religious’ thing. If so, I doubt whether it will find many converts among contemporary biologists.</p>
 3624: <p>I agree, and dont think that LaTeX-use should be "mandatory". I like and often use LaTeX for equation, but one additional problem, besides the formatting you mentioned, is that it is often rendered incorrectly on mobile devices . For instance, in the answer to the Q you link to I see this (Xperia/Chrome):</p>

<p><img src="https://i.stack.imgur.com/N9lHCm.png" alt="enter image description here"></p>
