That’s all in the article. The author goes into the confusion that it had the Apple logo on it.

Win was conceived as a modifier reserved for the OS (not to be used by applications), while command never was. Command is for commands. If you come to the Mac from Win or Linux it often helps to think of command as what ctrl does on those systems. Ctrl on the Mac started as Terminal-Emulator specific modifier— Which to this day is great, because your universal copy shortcut (cmd-c) and interrupt (ctrl-c) are different things.

Indeed one would map win to command, but only because you need another key for a modifier that‘s not ctrl or opt/alt, conceptually they are different