For instance multi window apps can’t tell the compositor where to put their windows

They can have positions lf existing windows saved and restored (still rolling out), and I think can ask for some details of initial placement outside of that too.
Of course still very limited and not handling the specific cases you mentioned.

registering global hotkeys

Setting up hotkeys is possible, just in a very different way. You have to have the desktop environment forward it, and for now specifics differ from de to de. Generally they can all bind actions though. A safe minimum-viable way should be to add shortcuttable actions to the desktop file I think, though the qt shortcut stuff should also generally work I think.

overscan correction

kwin at least has had that for a while

Personally for me I used to have a script invoked by tilting the sceoll wheel that'd send a shortcut (e.g. ctrl+page-up/down) to the window under the cursor without focussing it, letting me change tabs of unfocussed windows.
I think I did that by quickly changing input focus, sending it, then changing it back, with xdotool etc..
On wayland I've tried implementing that via kwin scripting a few times, but found it so hard to debug and to work with in comparison I never managed to recreate that simple tool.

Having universal posix-like tools to affect the window manager and user input from console is definitely something I miss occasionally.
Largely this is just a lack of wayland tools I am sure. And I must admit it's been a while since I last tried.