For electron, if ELECTRON_OZONE_PLATFORM_HINT and electron-flags.conf don't work, you can also add --ozone-platform-hint=wayland to the end of Exec in each .desktop file (also works on Chromium, but not CEF AFAIK and sometimes CEF).
There's also --ozone-platform-hint=auto if you find yourself switching between X11 and Wayland.