Was it ever an issue before? XBL integration is handled by the game and XBL API, Steam is irrelevant there.
Microsoft created a Steamworks <-> XBL API that was beta tested in Rise of Nations' UWP release and subsequently implemented into the Steam release of Killer Instinct, but all other Steam releases of WinStore games use Steamworks. MCC will be the first game with some level of XBL integration (probably Uplayesque).