Using the Live APIs to provide achievements, connect to Xbox friends, etc. just isn't really relevant to my mind. I'm happy (assuming it doesn't break the game like it often did in GFWL) if they want their PC releases to hook into that stuff, and there's no fundamental reason (besides Microsoft purposely restricting their own APIs) that a game can't do so and still be released as a normal PC executable.
I am not an IT expert but surely if they released a game as a "normal" PC game i.e. modifiable and hackable, then there is no way on earth they would want to connect that to their Xbox live ecosystem.
People would immediately have gamerscores of many millions, plus start sending spam messages about free ipads and large male members... Sure on one level that doesn't matter at all, on another level it matters an awful lot.
Talking more generally - rather than the post above..
The Xbox ecosystem is very closed with all the pros and cons of that - an awful lot of people value the pro's over the cons. That very closed ecosystem is being nudged over the hardware border into the PC world, which is full of people that have a very different set of pro's and con's.
That's going to cause friction but it also increases choice. Sure people may want "normal" versions of tomb raider of Quantum Break, but their current choice is Windows store or none, and there are perfectly sensible and valid reasons why that is the only choice available, and probably will be for the forseeable future.
I think it's good to call out reasons why this is a bad choice, or technical issues of how the store version of the game doesn't work as well as the "normal" steam version, and hopefully MS will improve it off the back of these comments.