z ordering for text tool popup window does not exist. any other modal window (that is modern style, save file does not exert this behavior) goes below it. try to exit with unsaved changes and drag it "over" the aforementioned popup.
altho, if you click the (disabled) main window and focus modal again, then it goes over the popup. maybe that's why popup disappears and appears again when you open a "native" save dialog /s.
don't worry tho, the popup is not disabled by itself. so you can click a combo box, and it has a separate z order! imagine how many combinations of windows over windows you can get in this way (it's 3).
i tried recreating this behavior in wpf for 5 minutes with no luck (i think new mspaint uses winui3 but i ain't installing that), so i assume it's either complete incompetence or newer microsoft ui frameworks being worse (who would have thought).
ah, almost forgot. combo box doesn't close if you click on a non-interactive part of the text tool popup. in other parts of this app it works the way that any other windows app does. maybe it's because it has editable text? just a guess...
besides that i have have some issues with the ux of the redesign, but these are more subjective so i'm saving them for a separate time.