Given the press MS has given to patent license agreements with Android OEMs, I would have to think that it would have trumpeted any such agreement with Google. Since it has not, I have to believe that no such agreement has been made. Given the usual claim by MS-boosters that MS is merely trying to "protect its intellectual property", it is rather curious that MS has never even threatened to sue Google over the supposed patent infringement; it leads me to suspect a lack of confidence in its claims as Google has deeper pockets and a bigger commitment to Android than do any of the OEMs; and is therefore much more likely to fight a lawsuit.
It has been surmised for some time that MS' VFAT patent is the reason wny many Android devices (such as my three year old Samsung Galaxy Nexus 2) do not have SD card slots, but that has never been publicly acknowledged. It curious, though, that MS has never even threatened to sue Linux distributors or the Linux kernel developers over the same issue (support for VFAT is in the Linux kernel distributed with Android, not in Android per se).