Anyway, keybindings are certainly changeable if you're ready to dive into a hundred distinct projects each defining their own key handling. There's no truly system wide way to alter system keybindings in any meaningful sense.
Currently I think KDE is the least-bad option, as common shortcuts can be remapped globally, but it could be a lot better — Qt can universally remap ‘Control’ shortcuts to the GUI key, but it's only available on Mac builds.
For example, I use Super for tiling window management, launching programs, and other things. On macOS, with Yabai and skhd, you can't use plain Cmd to do that.
Overloading Ctrl has downsides, but I think it is a net benefit overall.
Anyway, you can use cmd, you just need to have an actual command (non-modifier-key) to pass it—I have no use for a key that does one thing.