system
Given the following post, respond as if you're commenting on Reddit:
human
[Yet another WH40k] Why'zit that those Mechanocus Priests or whatever worship their own cult gods? I don't know a ton about the Imperium but their god emperor shouldn't be okay with them not worshipping him, right? Shouldn't that magic wheelchair god consider it heresy?

(I'm not good at writing in character, especially when I don't know a warhammer from a fortythousand)
gpt
Just an FYI, if you have a question you can just ask it. It can sometimes be fun for some people to do in character stuff, but it's far from necessary.

As to your question, the answer is that it's complicated. The Adeptus Mechanicus technically worship what they call the Machine God. However, when the Emperor first arrived on Mars his incredible understanding of technology led to him being revered as the Omnissiah, the physical avatar of the Machine God. 

As to why the Emperor didn't care about them being so religious and the Ecclesiarchy not caring about them following the wrong religion, the answer is that they're so indispensable that they get to do pretty much whatever they want. The Imperium would grind to a halt without the full cooperation of the Tech priests, so they get to directly oversee their Forge worlds, keep their religion, and answer to pretty much no one but Inquisitors and the High Lords of Terra as long as they pay their taxes and build stuff.