Microsoft desperately wants to become a services-based company. It's been on their game-plan since the early 90s (at least!) and they have been incrementally moving the company - and their customers - in that direction ever since. For a long time, everyone - including Microsoft - assumed that the ultimate goal was to charge a yearly - or monthly! - fee for the use of their software, be it their Office productivity suite or Windows itself. Initially they were hamstrung both by the lack of infrastructure (e.g., high-speed internet) and customer acceptance (outside of corporations, the idea of "licensing" software - as opposed to buying it - was absolutely foreign to people). Nowadays, with high-speed downlinks and almost two decades of slow-but-fruitful customer education, neither of these problems are as much a roadblock as they were before, and we've already seen Microsoft dip their toes into service-based sales (e.g., Office 365, as one example). But as the importance of desktop PCs and operating systems decline, recent indications are that Microsoft is becoming less interested in monetizing their own software as they are in creating a platform where they can monetize OTHER people's software. The massive buildup of Azure and the pushing of the UWP platform are the two most obvious examples of this strategy.
Ultimately, I think that Microsoft will license their "client / store" for free so they can grab the services fees, even to the point where their reliance on Windows becomes a secondary consideration. That's right; I forsee a day where - if they can get UWP running securely - we might even see Microsoft-blessed apps running on Linux (as well as MacOS, Android, and any other system they feel they could monetize). The Seattle behemoth is transitioning itself away from its Windows monopoly (not entirely without resistance from within) because they recognize that - long term - remaining an OS developer isn't going to be a viable strategy. I think this is a major reason that the Windows10 upgrade was released for free (and why Microsoft pushed so hard with the XBox and Windows Phone), as it greatly increases their potential market (a lot of Microsoft decisions start making sense if you ask yourself, "long-term, does this help Microsoft move towards a services-based business?").
Obviously, third-party store-fronts like Steam challenge this goal, so while I don't necessarily believe accusations that Microsoft are sabotaging their competition, it wouldn't entirely surprise me.