Howdy, I can see that because 'modern' apps like to paint themselves all over places like the titlebar of windows, we now have situations where that can interfere with windowblind skinning.
I notice there has been work specifically to handle/skin the explorer window, might there be some intention to perhaps provide a 'app template' type border skin definitions that we can assign to other problematic ones?
A couple of things seem to happen, like the app drawing its content 'before' the frame, and so end up 'under it' partially - this seems to be affecting a good e.g. the W11 settings app where the search control is usually partially obscured. Explorer at least ends up on top.

All of them seem to 'respond' to the 'Caption Size' setting, where if you *increase* the value, their content shifts *upwards* - so it appears internally windows is essentially saying to apps 'move yourself up this much to cover the existing caption bar' - if you set it to zero, you can push the content back down again but unfortunately it won't adhere to negative values, so you can't force the content enough lower to prevent *any* overlap.
The first level of images here are using 0 and the others a positive value - can see that where the 'modern' app decides to start drawing is roughly the same point across all the windows.
I think windowblinds going under like it does for explorer and the phone app is the better option, and then maybe a custom 'modern app' border specified which is styled to surround more nicely these apps that shift themselves upwards.
I don't know where the 'default shift value' is coming from in the OS too, clearly big fat top borders still affect where the client area and internal non-client area positions start, but you can't get rid of it completely e.g. by making a fat frame with transparency at the bottom - the painting gets corrupted in various ways. Maybe there's a 'minimum' OS Caption size or some other metric we can tweak?
And why does Settings under but also has a weird little 'light blue solid gap' (you can *just* see it in the bottom row) painted when caption is 0, obscuring even more.
Maybe as it seems to be an almost fixed value, Windowblinds could just avoid painting to this region at all as an option for some apps/windows, negating worrying about over/under at all?
I know this is not really Stardocks 'issue' - windows is clearly just deciding to let apps break previous paradigms and there's not standard which makes standard replacement harder.
And of course app exclusion is a thing - but be cool if we could nail down the majority reason and get some general approaches for them.