On balance, I really like that Ctrl is overloaded in that way. Means that Super/Win/Cmd can be used for a wide variety of things on top.

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.

I mean yea, but in practice I run into frustration that the terminal doesn't have a key dedicated to commands far more than I need to do something globally.

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.

The problem is that many apps on macOS use Cmd + one or more other modifiers for their own shortcuts. On Linux at least, no apps that I know of use Super in any shortcuts.

It happened because Windows adopted IBM CUA, and the ‘desktop Linux’ crowd had a fetish for copying Windows. Before that, X11 programs were typically fully configurable, with key bindings in X resources.

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.