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FYI: You can enable them in Gnome with Gnome-Tweaks. Apparently a very recent version of Gnome dropped this functionality for reasons that are beyond my understanding (but that's often the case when I look at the decisions that the Gnome devs make).
However, getting the Control -> Command/Super thing to work is much trickier. The best way is to use this: https://github.com/mooz/xkeysnail
However when I tried that, I ran into all kinds of weird behaviours all over the OS. Also, it doesn't work with Wayland.
Have you tried https://github.com/B00merang-Project/Windows-95 or any of the similar themes by that project? There's a bit of extra padding still but it's vastly more usable than the Adwaita default. (And of course you don't need to bother w/ the retro icon packs shown in the screenshot, the basic GTK+ theme is plenty enough.)
Another option is https://kinto.sh . It worked perfectly for me out of the box on Pop OS, and with a few tweaks to shortcuts I’m pretty happy with the experience to the point where I can fairly seamlessly switch between computers and not be driven crazy by the shortcuts.