Yeah, I think OP is right that this behavior is confusing for Windows users, but as a longtime macOS user I don't find it confusing or problematic at all.
I'm more a unix user than a Windows user. I use pretty much all current OSes (including Mac and Windows) on a daily basis but FreeBSD is my daily driver. I think macOS is pretty unique in this regard (as well as being the only that use Meta-C / Meta-V for copy/paste, something that still bites me every day as I switch between OSes :) ).
But I only used macOS since 10.2, never used classic.
I had the same issue with copy/paste on MacOS, until I couldn't stand it anymore and used software to remap the keys. I swapped the builtin Fn, Ctrl, and Meta keys around so they are positioned like you'd expect on a normal keyboard (and a normal OS), and it instantly fixed my issues without any other negative side effects aside from having to learn another key combo for Ctrl-C in terminals.
Classic was the same. On older systems, I think it was a good idea, given the speed of hard drives back then. With SSDs, the performance gains from keeping unused programs alive are far lower, but at the same time, RAM is far more plentiful, so it comes at a much lower cost.
Considering Apple added the Command ⌘ key in 1984 and the original cut/copy/paste as being command-x/c/v, it's more like the others didn't follow convention at the time.
