I just got a PC for the first time in a (very) long time, and got a Ducky One2 keyboard (Windows layout) to go with it. I ended up liking a mechanical keyboard more than I thought, so I wanted to use it with macOS as well.
Using the Modifier Keys setting in macOS worked great for just about every app except AnyDesk:
However in Anydesk, while controlling another macOS machine, it wouldn’t see the Command key anymore. Shortcuts like Cmd+Tab, Cmd+W to close a window, or even Cmd+S to save would all happen on the host machine itself (ie. Cmd+W would close the Anydesk window, and Cmd+Tab would switch to another application on my laptop).
The solution was to switch the Modifier Keys settings back and download Karabiner Elements, then use that to switch Command and Option (Windows and Alt on the keyboard) instead:
Success! Now Cmd+Tab (or Alt+Tab on the keyboard) switches windows inside of the remote controlled Anydesk machine.