I’ve snooped around a bit and I’ve noticed something:
For one, Firefox does not seem to be installed as a Flatpak but still exhibits this behaviour
Secondly: Gnome applications installed via Flatpak don’t seem to have the same problems. It’s only other applications like VSCode, Signal or Insomnia that have this problem.
For these applications I have also noticed that if I remove the permissions for X11, the app doesn’t start anymore, leading me to believe that these applications are using XWayland
What this looks like to me is that applications that actually use Wayland as a windowing system don’t have a problem, but applications that use XWayland do have the problem. Now the question is… how do I fix this?^^ I know there’s technically xinput where you can remap some keys, but I don’t even have xinput installed and I don’t know if this also works for XWayland