I think this is probably company politics at play. Microsoft, particularly the business unit (the Windows Division) which runs the store, wants the lucrative retailer cut on software sales that they see Steam taking for games and Apple taking for iOS and Mac App store. That scale of profit margin absolutely dwarfs the entire Xbox business.
I can imagine the larger business units are able to exert pressure on the Xbox Division to restrict games to Microsoft's own store - at least in the short term - as a leverage to get consumers into the store, which is generally the biggest hurdle any new store has. People are largely creatures of habit and shop where they are used too. What drives them to new places is lower prices (which the Windows Store doesn't have) or exclusives. Hell, the whole pivot of tacking on Windows support for Microsoft game exclusives may be driving this as well. Just because a business decision impacts Xbox doesn't mean it's necessarily about Xbox.