You need Windows to run it... Do you think MS really cares if you buy it for X1 (owned by MS) or if you buy it for a Windows 10 based PC (Which MS owns the OS).
MS games are more Microsoft specific exclusives. That's like saying when a game comes out for the Vita and the PS4 it's no longer a Sony Exclusive, because you don't need a PS4 to play, but Sony owns both platforms......
Just like MS owns the X1 and the Windows OS the games will run on. Either way MS is getting the money... and the cross-play (X1 and PC) will make the experience that much better and makes even more sense now than ever for MS to release games for the PC and X1. This will only increase MS games profitability by vastly expanding the user-base.