system
Given the following post, respond as if you're commenting on Reddit:
human
My supervisor wants me to modify an article we are writing in a way I don't completely agree with.

As part of my work for my PhD I wrote a scientific article.

I am the first author, my supervisor and two other staff members at my university are authors, too. I wrote 95% of the article by myself, then I sent the draft to my supervisor and the co-authors and everyone proposed some changes.

A section of the paper I wrote has been introduced after I had a discussion with professor X, at university Y (not my university). Even if I didn't see it at first, now I am convinced that the additional treatment in this section is needed to be able to get realistic data. If we don't do it, then we are not modeling a fundamental feature of the system.

The point is that this section doesn't make our theoretical predictions any better, in most cases they are even worse. I addressed this point in the paper, and I concluded that another approximation we are doing is critical: that one must be the culprit for the disagreement. There is also consensus in scientific literature that the aforementioned approximation is critical. It's too complicated to remove this approximation, it's very commonly used but in some cases it might fail. 

I proposed that we keep the section, motivating my proposal: I am analyzing a fundamental feature of the system. If we neglect that we may have a slightly better agreement by pure chance, but our description is farther away from reality.

My supervisor has become really aggressive at this point. Usually he is very warm and welcoming in his emails, now he's been criticizing me for everything, like the indentation of my LaTeX code, or the legends of my plots. He made fun of me for being "emotionally attached" to my calculations, even if they are (in his opinion) useless for the paper. We discussed a lot about it, and in the end I wanted to keep the section, while, on the other side, the other three co-authors wanted to remove it; they didn't have any scientific reason to trash it.

My supervisor sent to me this morning his final draft, and the section is nowhere to be found. He wants a comment on that, and then we can submit it.

What do I do? I think that my paper is quite decent even without that section, however I feel like we are not being 100% honest. I explained very clearly my point of view, many times, they know that I don't agree with them; I feel like I cannot insist again on keeping the section. Also, we informally voted on that section and it's me (a PhD student) against a professor and two staff members.

I see no way I could further insist: the general feeling is that we discussed, and my proposal lost...

Also I am now visiting professor X, who suggested the improvement, at university Y; he asked for a preprint of my article. I am a little bit ashamed of showing it to him because he is mentioned in the "Acknowledgements" section, and we thank him for "fruitful discussion", even if now we are completely neglecting his remarks.

Also I have to give a seminar soon at university Y. Am I going to present something I am not fully convinced of? Or am I going to contradict my most recent article in my talk?

Sorry for the wall of text, thank you for your answers!
gpt
Give them a chance. You are an apprentice now, they are masters. The very idea of apprenticeship is that you look at another person, a more experienced person, and try to remember what worked for them, and what did not. Once you are a master yourself, you'll play by your own rules.

Remember their decisions, and their rationale for making these decisions. Later, try to understand whether these decisions were right or not. For example, one of the reviewers may ask exactly for a discussion like that, so you'll bring it back. Remember all that, so that you could decide for yourself in the future whether it was a right approach, and whether you'll follow it when you are independent.

Another option, consider publishing this piece as a micro-article of its own. Is it possible? Pick a low-impact factor journal, add a bit of data here and there, and publish it separately (a separate paper, but keeping your supervisor as a co-author, probably, unless they explicitly bid out of it). Oftentimes it makes a paper better if it is published in pieces.

Science is not only about getting an interesting result, it's also about popularizing this result, and explaining it to people. Explaining things in a way that makes them understood is as important in science as getting the results themselves. And for reaching this goal sometimes, for the sake of clarity, you have to streamline your work, sacrificing some tangentials. Most successful researchers often manage to turn these tangentials in projects / publications of their own, but that's a separate story.