I think you misunderstood. Control, alt, meta, hyper, and super are (at least on my current OS) distinct modifiers. There are also keys bearing some of those names on most keyboards which makes things confusing to talk about.
Each modifier can be mapped to any physical key. For example, I'm one of those control as caps lock people you mentioned. I then have hyper on the left control key, alt and meta (yes both) on the left alt key, level 3 on the right alt key, and compose on the right control key.
I've never seen a keyboard with hyper or super. I doubt many people have, since they were only present on hardware obsoleted decades ago. Meta, aka the windows key on most PC keyboard, is usually present, but most people wouldn't know its name. On Windows, it's not even usefully bindable since Windows uses various shortcuts for it by default. On Linux, it's not bound to Meta by default by most distributions. So for the vast majority of people, it's just Alt.
I don't think Emacs has done itself any favours by using obscure and non-standard terminology based upon machines from the '70s which few people have heard of, let alone experienced. For the vast, vast majority of us, we all have bog-standard PC or Mac keyboards, and have done for the past 30+ years. It would have been in everyone's interest to standardise on terminology and keybindings which were immediately understandable and usable by all.
Given that every other application uses the standard terminology and keybindings, and that I don't see much in the way of compelling advantage to keeping the non-standard bindings other than habit, I think preserving backward compatibility for four decades was laudable but misguided.
Neither have I outside of photographs! The trouble is that they did exist previously and X11 settled on an abstracted model that supports 5 modifiers (in addition to control, shift, and lock). You have to bear in mind that Emacs can't just stop supporting certain (now defunct to the mainstream) modifiers as many users have setups which depend on them.
I suppose that cosmetically they could update the documentation by changing M- to A- or Alt- or something. Would it really make a difference though?
Aside: Not meaning to be pedantic, but at least under X11 Super is the "Windows Key" and Meta doesn't exist by default. I just checked and (on my machine) the keycap with the Windows logo maps to X11 keycode 133 (hardware specific) which produces keysym Super_L at both levels 1 and 3 which in turn maps to mod4.
Unfortunately I didn't notice your reply earlier (the consequence of being productive).
Rereading my previous comment I've realized there are some slight inaccuracies - keybindings are conceptually a bit complicated (at least under the historical X11 model). My Alt keycap actually just produces the corresponding Alt keysym, which maps to mod1. My confusion was due to the Meta keysym also mapping to mod1 (this is the default configuration) even though no key on my keyboard is currently configured to emit it. I set everything up quite a while ago and then forgot some of the details.
* Caps Lock -> Control: This is simply more comfortable for frequent use, particularly in combination with the Vi directional keybindings (hjkl).
* Right Alt -> Level 3: AKA AltGr, this is useful for entering common Unicode characters.
* Right Control -> Compose: Useful for a number of other Unicode operations. I don't seem to make much use of it in practice though.
* Left Control -> Hyper (-> mod3): I had a free key. This gives me an extra modifier for use with things like my window manager that's pretty much guaranteed not to conflict.
* Shift + Space -> Underscore: Makes C programming _way_ nicer.
* AltGr + Space -> Nonbreaking Space: I don't actually remember why I configured this one. I never use it.
* Shift + Shift (ie left & right) -> Caps Lock: I don't actually use it, but this way it's still available.
