There are applications that do not run as a window, in present I have a global shortcuts that run a bash or python script, I know I am a power user so I will need a way to whitelist my use case.
GNOME and I'm pretty sure KDE too has a method to set custom keyboard shortcuts that can execute commands.
Yeah, that is the problem with Wayland: the solution to many missing features you get out of the box with X largely depends on the environment you are using.
Wayland needs to offer full access to "power users applications" if not we end up where Windows will be more friendly for the users that need this type of applications