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Meta, Hyper, and Super were all originally different keys. See this lisp machine keyboard from in the 70s that had 7 modifiers, including all of those. Most of the time Hyper or Super are mapped to the Windows key. With Meta it varies more from program to program. A lot of desktop software maps it to the Windows key. In Emacs its usually mapped as Alt or the Esc key.
I’m not sure if it’s directly mapping the input. I think it’s getting the other keys input and binding it to the same commands. Also, Emacs was around even before the X windowing system, so they probably came up with the mappings before a lot of these common defaults came about.