You can’t, basically. The copy key isn’t configurable for example, you’d need to rewrite the apps from source to achieve this. Some dynamically link to shared library UI toolkits that you could patch, others implement it themselves… it’d be a never-ending game of finding new broken apps and fixing them one by one (and that’s for open source apps, forget closed source ones.)

You could map Cmd to Ctrl but that only fixes copy/paste, but now it will send a SIGTERM to the terminal on Cmd-C now, which means that’s still a pain.

You could write some custom keyboard driver that intelligently maps the command keys to the right keys the app expects, dynamically based on some rules, but that sounds horribly brittle and likely unworkable.

I agree. I really like the ALT shortcuts on Haiku, and I remap my external keyboard on macOS so command is mapped to ALT rather than Super.