Sounds like your issue is mostly flatpak, to me.

Only issue I have with drag and drop is any wine game I am playing assumes the file is for them, and jumps to the foreground if the cursor passes over it while dragging. If I accidentally drop it, dragging stops working in the drag source app. Sure, this wouldn’t be an issue if I were not sharing and moving files mid-game, but that is my wont.

I have had situations where I’ve explained this multiple times to people while helping them manually install the DXVK Async fork into their wine prefix and they still get it backwards.