Isn't the Macintosh desktop (with Cmd as the modifier for standard shortcuts) older than Windows and Linux desktops? So historically, it's not Apple that deviated but the others?
(I did not do an extensive search into this, so there might be Ctrl-based standard shortcuts that predate Apple.)
Apple moved the Ctrl key around at least a couple times. On the Apple II it was next to the A key, the same as it was on the Xerox Star. The CMD key was a later addition.
At this point, I'd say let history be history. It'd be better to standardize on what most people are using.
Yes, the Cmd key has been around since 1984.