Is this infringing on any of Microsoft's patents? And if not, why is Microsoft allowed to collect royalties from Android OEMs who support the FAT file system?
It's quite possibly infringing, but it's unlikely to become a target for a lawsuit unless it starts making a lot of money or starts hurting a good percentage of sales of MS products.
You are allowed to do anything. Microsoft tried to collect royalties and OEMs let them. You could try too. Good luck!