I don't think Microsoft has been bothered with the Amiga since Windows 3.1 - they had the business and office markets and they knew it.
When that was all going down I had to reluctantly switch to Windows to continue taking work home with me.
Even then the only thing I ever heard that was a thorn in Microsoft's side was that Doom was installed on more PC's than Windows 95 - and actively pushed for Doom to run on it.
In 2000 I heard of them doing a push to compete with Linux on the server front... but I don't think the Amiga has bothered them for a very long time - and if you try and see it objectively from their side, there's no need for them to be.
Apple has once again risen as prime competition for them, and the Amiga is a looooooong way from that, even with the recent releases of hardware/software.
When it comes to companies buying competing products - Avid does this fairly aggressively - buying up companies for the sole purpose of discontinuing competing products (Newsstar and SoftImage spring to mind) - but again I can't see Microsoft being bothered as the Amiga is hardly a blip on the radar anymore... Everything classic Amigas used to do have long been 'absorbed' and can be done better for less money.
I don't know how much Amiga Inc would need to make to stay afloat - seeing how they seem to do very little actual development of their own, maybe they dont need much at all...
Still there is another scenario - corporations do buy companies that are never meant to make a profit, to be used for tax write offs and incentives... this, to me, seems a pretty likely thing as I've never really heard of Amiga Inc turning a profit in the last 5 years, in fact I've not seen bleep out of them other than the lawsuit....