Apple also invented their own key “Apple” now “CMD” for operation like copy / paste to explicitly not have the issue to overload the already know escape sequences. Windows being on a system without a normalized keyboard had to reuse keys that are common to keyboards used back then. Vertical integration played into apples cards even back then.
The location of the command key is also a lot more comfortable. Thumb vs pinky.
Aren't the Apple key and the Windows key just corporate branding on a super key?
I setup my Linux system to use it because it's more consistent for copy pasting in a terminal.
With regards to the windows key, I have grown to appreciate it, I am on a X11 desktop and map all my window functions to it which makes a lot of sense, then ctl and alt can be freely used by applications however they like. I suspect this is sort of what microsoft wanted when they specified it but were hamstrung by their own backwards compatibility(they were not able to make the hard decision to move close to window+f4 for example).
The otherwise useless context key makes a great compose key.
On a theoretical level one would almost want one dedicated control key per level(os_key to send commands to the kernel, window_key to send commands to the windowing system, program_key to send commands to applications, user_key reserved for user custom bindings not to be pre bound by applications) I am not sure what role chording should have under this scheme. allowing a higher level to use the lower level button? a window manager cannot use os+key or app+win+key but they can use win+os+key. an app could use app+win+key. I would also like a unicorn, oh well, fun to think about.