There is no standard way to register global keybindings under Wayland yet, but this is bound to happen eventually. Not as a builtin part of Wayland, but it doesn't matter. It will of course use D-Bus interface, as KDE does it now for example - but if an application doesn't support this interface, it can't steal keybindings, it just doesn't get to install global keybindings itself.
Not sure what you have exactly against D-Bus, but clearly modern Linux desktop embraced it.
In the desktop things, that wayland aims to do, dbus is useless. (actually i don't know what it's useful for at all, other then quickly hacking some object oriented (gui)client-server desktop program)
I do recommend reading the dbus protocol (the protocol, not the API).
Sorry to sound negative but "modern linux" now means "desktop crap", and it is all crap. Freedesktop.org (the linux "desktop" "standards" authority) has gone from "ehh, passable" to "complete crap" in the last... idk 5-10 years (the "desktop" quoting is because it has gone pass the actual desktop problems).
From that point of view, "Wayland" is kind of a short-hand for a number of different stacks that have some components in common, and speak the Wayland protocol. If you choose not to use a complete stack on a system, then the result can't be fully functional.
Personally, I don't have any sense of how much dark matter is in the area of Linux GUI applications. We can easily know about Open Source, where most modern applications sit on toolkits and desktops that are moving to Wayland, but presumably places like CERN have some really old internal applications that will only ever run on X until they are replaced. I'm genuinely unsure how large that problem is.
I have to say that I'm always skeptical about arguments that something can't be done for performance reasons. People have been using that argument against new technology since at least the days when C was decried as new-fangled, decadent luxury.