"Meta" usually refers to Alt on Linux systems with IBM-PC-derived keyboards. When I look at `xmodmap -pm` on my system, the Windows key is referred to as "Super".

That's a rather arbitrary binding; some keyboards have a discrete meta key. No reason to use super if you're not targeting windows!

Alt had already been used to replace meta by the time the windows key came about. Therefore they mapped the windows key to super.

You can blame Emacs users.

https://en.wikipedia.org/wiki/Super_key_(keyboard_button)