There is one standard and single simple answer: xdg-desktop-portal with pipewire. Some compositors might have implemented their own private APIs, but that is not a standard by definition.
Global shortcuts are a bit more thorny, exactly for the reason you mentioned. You present one POV, the another is, that application-defined shortcuts are incredibly hostile, as they allow application to stomp on each other in the better case, or hijaack global state in the worse one. Some other operating systems do not allow it either, for the same reasons. The long-term solution could be defining api, that allows application to advertise global actions, and allow the user to configure shortcuts that might (or might not) call these, in some user-friendly way.
> A portal frontend service for Flatpak and possibly other desktop containment frameworks.
When it comes to global shortcuts, I'm not saying it has a super easy solution, but it's something that it's essential to support. Wayland intentionally doesn't, and I can't see that changing in the short term (as you also agree)
It is dbus api, and is able to work cross-namespaces (i.e. flatpak containers too). There no harm in using it in non-flatpak apps, at least you will be ready if your app ends up in flatpak.
Wrt global shortcuts, I see that there is some work done. The intentional part isn't malice, as in not willing to implement it at all. It is about not implementing temporary solution, that will be quick and dirty, and then being stuck for supporting it for next 50 years.
It took Golang 12 years to attain generics. Wayland is already 14 years old.
To tell the truth, X11 took roughly 10 years (1986 to 1996) to get to a pretty usable, while pretty imperfect, state, and largely dominate Unix desktops.
Global shortcuts are a bit more thorny, exactly for the reason you mentioned. You present one POV, the another is, that application-defined shortcuts are incredibly hostile, as they allow application to stomp on each other in the better case, or hijaack global state in the worse one. Some other operating systems do not allow it either, for the same reasons. The long-term solution could be defining api, that allows application to advertise global actions, and allow the user to configure shortcuts that might (or might not) call these, in some user-friendly way.