For anyone looking for a temporary workaround:
This is not at all elegant nor safe in the longterm, but the binary responsible for the pop-up is called “gnome-control-center-global-shortcuts-provider” and the rest of Gnome functionality doesn’t need it to work.
Locate it within your system and move it to your home folder or any location where you can safely restore it from in case you need it again which you can do by just moving it to the same folder it was in originally.
Keep in mind that any update to gnome or the gnome-keybindings packet will generate a new binary in its originall place. You can just repeat the process in that case.
I also don’t think it’s right from Gnome to put all the blame on app developers and I think that a safe solution for the user side should be provided.