I've been looking for a way to do this myself. Nothing I've tried so far has worked but if someone from Stardock could answer a question for me I think I can get it figured out. Can WindowBlinds exclude something triggered by another application? It seems UWP apps are controlled by a host service so blocking that alone might create other problems.

Any updates on this?

I guess I'll just keep waiting. You'd think this would've been something figured out a long time ago...

Thank you for the update. If we want to exclude all UWP apps, which process/executable should we exclude?

Excluding svchost.exe did completely crash explorer at first and I had to do a full restart. But after a restart UWP apps were actually *kind of* excluded. However, now there's an ugly white border around them, regardless of what theme is used. I wonder what's causing this and if it is possible to get rid of it. 

This excluded all UWP apps from skinning perfectly. Thank you very much!