Thank you OP. I read the article.
I think Microsoft, as a video game publisher, has a right to protect their intellectual property. If that means a non-standard (specifically non-EXE) PC application that's distributed through an official Microsoft store, they're allowed to do so. Additionally, UWA sounds like a set of tools for making software, not unlike CryEngine or Unity. Microsoft should be allowed to use and promote using these tools, even if it means something like lack of mod support in games.
What would be unacceptable is if Microsoft would one day force all Windows apps to be made with the UWA toolset, and sold through an official Windows store. But that is ridiculous. We're too far down the Windows PC path too assume that could happen. For one, developers wouldn't stand for it. If you're already familiar with a different toolset (or have built one in-house), you wouldn't suddenly want to learn something different. I don't think gamers would stand for it either. Valve has made a big push to make Linux a strong platform for games, and you can currently get over 1500 Steam games on Linux (including big name games like Borderlands). If Windows became closed and proprietary like iOS, I think gamers would jump ship to Linux (or maybe Mac).
To make Windows a walled-garden-type platform would be doing a disservice to a large number of people who buy Windows: PC gamers. I just don't see it happening.