Is it really about these particular patents? MS may have got away with licensing / bulk cross-licensing in the past, but surely MS don't really believe all these will stand scrutiny!
It seems much more likely that this is about the legal fight. Its MS saying, license Windows or there is a good chance we'll dig up some patent which we can use to take you to court. You might win, but in the meantime it might affect your stock price to be sued by us. Are your lawyers so cheap you can afford the fight? What if your legal team isn't as good as ours and loses? Its so much easier, safer and cheaper just to pay a small sum as insurance against all that nastiness.
MS can afford to lose all of these patents and they still "have x hundred infringed patents" they could use to come at you.
I can't imagine a vfat patent license (or even all of them together) is going to make a whole heap of difference to MS' bottom line. It makes sense to try to get it invalidated though, to squelch the FUD and give others confidence.