The junk apps you mention are already violating trademarks and copyrights, so Microsoft should just make it easy to report those violations and get the apps taken down and added mechanisms to prevent those junk apps from reappearing, like blocking all "Inkscape" apps except the one from account of the trademark holder.
If their concern was the different price between the app store and other ways to get the app, then they should have simply required developers to refer to those other ways from the app store itself, or allowed developers to set an app as pay-what-you-want plus the Microsoft cut, or both.
If that's the case, Krita would probably remain listed; it's unlikely to be reported as spam and is genuinely useful software, so the moderation team are unlikely to consider (letalone apply) this policy in relation to it.
That said, the policy is clearly not worded ideally if it puts a valid, legitimate app into violation. So it's good that the SF Conservancy are raising a concern about this (which it seems like the Krita developers have read[1], incidentally).
The metaproblem seems to be that we want people to install "the good, safe software" and not "the bad, harmful software" -- and especially not to pay for and incentivize creation of the latter.
Is that best achieved using moderation and written policies after-the-fact? Does the presence of absence of paid apps and in-app payments affect the alignment of incentives? Is there eventual, informed and communicated consensus from users about the best and safest apps to use?
I feel like we may be trapped in a local minima at the moment where a bunch of conditions around app stores are non-ideal.
[1] - https://twitter.com/Krita_Painting/status/154524168859936768...