As I understand Github is also run very independently from Microsoft in general.
MSFT's control isn't as "hard" as you portray it to be. At the senior leadership level they're pretty happy to allow divisions quite a lot of autonomy. Sure there are broad directives like if you support multiple platforms/OSes then the best user experience should be on "our" platform. But that still leaves a lot of room for maneuverability.
Soft control via human resources and company culture is a whole other beast though. There are a lot of people with 20+ years of experience at Microsoft who are happy to jump on job openings for middle-management roles in the "sexy" divisions of the company - the ones which are making headlines and creating new markets. And each one that slides on in brings a lot of the lifelong Microsoft mindset with them.
So yeah working within MS will be a very different experience for Altman, but not necessarily because of an iron grip from above.
Github operates independently of Microsoft. (To Microsoft's detriment... they offer Azure Devops which is their enterprisey copy of Github, with entirely different UX and probably different codebase.) They shove the copilot AI now everywhere but it still seems to operate fairly differently.
They didn't really fold LinkedIn in into anything (there are some weird LinkedIn integrations in Teams but that's it)
Google seems to me much worse in this aspect, all Google aquisitions usually become Googley.
Skype sort of became Teams thought, that's true.
Then the acquisition happened at a time when Microsoft presented a lot of opportunities to ship Skype "in the box" to pretty much all of MS' customers. Windows 8, Xbox One and Windows Phone (8) all landed at more or less the same time. Everybody's eyes became too big for their stomachs, and we tried to build brand new native experiences for all of these platforms (and the web) all at once. This hampered our ability to pivot and deal with the existential risks I mentioned earlier, and we had the rug pulled out from under us.
So yes I think the acquisition hurt us, but I also never once heard a viable alternative business strategy that we might have pivoted to if the acquisition hadn't happened.
GitHub Actions is basically Azure Pipelines repackaged with a different UI, so I don't think they mind much.
https://www.forbes.com/sites/louiscolumbus/2019/01/06/micros...
Believing that OpenAI is MSFT's sole move in the AI space would be a serious error.