Yeah I know that feeling. Thankfully, virtual desktops + 3 monitors has fixed that for the most part, but that's not always usable in some circumstances. I only posted that, as I only found out about it a month ago myself

The other thing I've done (with Zed in particular) is put the icon for the packaged app into my dock, so I can get to it quickly from anywhere. Of course, this becomes unwieldy if you have a lot of them in there!

Zed is also packaged as a standalone app now.

How many monitors/desktops are you running? Have you thought about increasing it?

I have 6 desktops running on 2 physical monitors and keep windowed things easily accessible. Nothing more than two swipes away.