The popup should be modal, nothing else should be able to steal focus.
If I remember correctly, the popup cannot be modal as when you switch between documents, you need the Scintilla editor to have focus. I don't remember why exactly, I can try.
Fixing individual issues is going to be a game of whack a mole because almost all of Geany is not written to handle it
This is the only case where dialog appearance depends on a key being pressed and its disappearance on a key being released. Nothing else needs to be changed. I don't completely understand why to defend a stuck popup being shown as something non-buggy.