You can also use EXWM in Xephyr, so you can have an emacs window with its own controlled windows instead of replacing the whole DE/window-manager. I suppose this doesn't work with multiple frames though.

I have been experimenting with xdotool windowmap/windowunmap and override_redirect (and maybe LD_PRELOAD?) to try get something like EXWM to work without creating another X server, by capturing windows. I'm doing this in vim though.

By the way, neovim has an apparently working EXWM-like plugin, NXWM/nwm: https://github.com/altermo/nwm