Stack Overflow was founded by Joel Spolsky, who is a Microsoft veteran from their era of peak dominance. I suspect it's a passion project of his that he'd like to hang on to, but he's also pragmatic and everything has its price. And it's profitable. I wouldn't be surprised if someone bought it. I can envision synergy between Stack Overflow and GitHub. Satya Nadella seems to really "get it", though, and I don't anticipate any dramatic changes to GitHub, or to Stack Overflow should they take it over.

StackOverflow has a fairly bad reputation despite its widely perceived usefulness (the community is often seen as toxic and hostile to beginners). Microsoft would have to severely invest into SO's PR and community management. Compare that to GitHub which has gotten over most of its bad press in the past.

It already uses Microsoft tech so why not?

Would be interesting but I don't think SO needs the funding / resources as badly as GitHub does.