What I do, is have a minimize keybind.
When I want to quickly do something with a window below the one on top, I hit that minimize keybind, do my thing, then alt-tab.
Unless I interacted with a third window, the one I minimized comes right back.
Or are you looking for something more like picture in picture? A pinned window you never interact with, only look at?
Edit: what if you flip this the other way around?
Make the windows you want to be interacting with transparent, and keep them on top. You'll always see the window you want to see, through them.