TL;DR: The Windows and Windows Phone ecosystems seem to be tied but neither of them are tied to the Xbox ecosystem except for a few "Xbox Live" titles that were released for Windows 10 and Xbox One (as far as I can tell, they're completely separate).
There is one massive problem with running Xbox games on Windows: virtually no computers have a Bluray drive. Not to mention, they won't because it would be a massive gift to the community in terms of circumventing the DRM. The higher ups at Microsoft won't even consider it.
Xbox Live games that appear in the Windows Store, Windows Phone, and Xbox One is certainly a possibility if not likely but, as I said before, the bulk of them will probably be microtransaction based. Microtransaction games generally aren't very successful on Windows.
Edit: Xbox app featured games open the Store program and it looks exactly like this:
https://www.microsoft.com/en-us/store/apps/farmville-2-country-escape/9wzdncrdqwjk
Which says right on it: "Works on: PC, mobile device"
Sooooo, it appears that for now, Windows and Windows Phone are shared for now and the Xbox app pulls games that were installed from Games for Windows Live or Windows Store. I don't think there are any Xbox Live games on Windows Store yet but that possibility certainly exists because the codebase is more or less the same.
Edit: Oh, the Microsoft Store does have a link for "Xbox apps." Uh...they're like...basic web content access apps...
Edit: I looked at some games that should be sharable between Xbox One and Windows (like Minecraft) and it appears that they're both completely separate for now.
Edit: The search for "
Minecraft" fails to find the Windows 10 version even though I was just looking at it five minutes ago. :\
Edit: Apparently it only exists in the Store on Windows 10.
Edit: I finally got it to cough up the URL:
https://www.microsoft.com/en-us/store/games/minecraft-windows-10-edition-beta/9nblggh2jhxj
For me, that links opens the Store app on my computer, not the URL but that might just be Internet Explorer/Edge that does that.
Edit: So I converted my Mojang account and got a free copy of Windows 10 Minecraft but now I can't figure out how to install or play it.
For the record, this version of Minecraft, it says on the store, is full of micro transactions. I wasn't kidding when I said Microsoft's store is all about microtranactions. And no, I'll never spend a cent on that bull.
Edit: Oh, I wasn't logged in. I had to click on "Free Trial" and it popped up a dialog to log in. Now it is downloading. I don't really feel like playing it but...it is clear this is a wreck.