Microsoft is in direct competition with Sony (XboxOne vs PS4). Also less less directly with Mac vs Windows, iOS+Android vs Windows Phone. I say less because this is about a physics engine used in games. XboxOne and PS4 are game machines where as those other platform have much broader interests.

If Microsoft either stops supporting non-MS platform or makes them 2nd class (new features first appear on MS platform) then yes, this is a huge problem.

Remember when EA bought Renderware back when tons of game studios were using it? GTA3 was written with it. Where is Renderware now?

It's certainly possible nothing will change but it's just as possible the glaring conflict of interest will influence things badly.