With regards to the paint.net issue, unfortunately that is entirely their end. You are right that for unknown reasons they draw solid coloured boxes over the titlebar. This is perplexing given on Windows 7 they supported glass frames just fine!
Apparently the developer isn't fond of anything custom theme related.
This can be fixed by modifying a single IL instruction, but doing so is against the program's EULA, so go figure.
Given that Electron applications also tend to peck at ...\DWM\AccentColor key for deciding on their titlebar colors, a semi-reliable solution seems to be to set the accent color to be as close as possible to the titlebar color and then use the second/third color to recolor your elements:

Generally speaking it is not possible to exclude a non UWA application from Curtains. This is because there is nothing to exclude them as the frames are a global thing. This isn't the case with universal apps as they have their own fake titlebars usually and Curtains actually disables that.
I suspected that this was the case, thanks for answering!
With MS edge, it shouldn't matter if it is beta or canary and we do not care about the install path. I have just checked here and both are respecting the settings set in Curtains as of todays latest builds. It may be how they are being launched thats the issue here? Are you launching them from a shortcut to the app (not a weblink) in explorer or via some other route?
This was apparently caused by
-disable-features=Windows10CustomTitlebar
which I have added while doing something with WindowBlinds and subsequently forgot about.
A new question: had the logic behind window frame drawing ever been documented anywhere? Testing with "fat frames", I can see that the top frame image gets stretched somewhat depending on added border width, but I cannot seem to figure out the exact height of window caption image frame for it to draw normally.