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.