Not surprised that the game is not Play Anywhere most likely.
It isn't a UWP title on Xbox One because it was released a long time ago when UWP didn't even exist. And considering it will have a Steam release, it all points to it being a Win32 game. I also don't remember if Microsoft ever added Play Anywhere support for such late ports. I think that all Play Anywhere games were released on both Xbox One and PC at the same time, but still UWP is the key here. Without it Play Anywhere is not possible.
P.S. On the side note, MS Store version should almost 100% have cross-save feature as Xbox Live supports it without Play Anywhere. For example, FFXV Windows Edition from MS Store supports cross save with Xbox One version. Quantum Break as well.
The default restriction is good for sensible apps like PayPal, but makes no sense for PC games. It's useless and makes modding unnecessary difficult. If Microsoft wants to deserve the trust and respect of PC gaming enthousiasts, they should get rid of it asap.
I doubt it is possible to get rid of it as too much changes would needed to be made to how UWP apps works in order to get rid of it. So, the best solution is to release a tool which will decrypt any UWP app gaining access to its content and then allow it to be repackaged. In order not to break security just disallow access to Xbox Live for such modded apps.