I would suggest that you try two things:
- Use an Apple keyboard with your Linux box.
- Configure your keyboard so that Ctrl is mapped to Command and vice-versa.
To accomplish #2 you need to change the keyboard mapping. There is an article that describes this process here: https://askubuntu.com/questions/131900/how-do-i-switch-the-command-key-and-control-key-on-a-macbook-pro
Even though the article is aimed at Ubuntu users, the tool it describes is the same in all Linux distros. This only needs to be done on the computer to which the physical keyboard is connected.