Yes, you can. OS X and Windows/Linux operating systems use different keyboard shortcuts modifiers for common actions, like 'copy' (Cmd+C on OS X, Ctrl+C on Windows/Linux) and 'paste' (Cmd+V on OS X, Ctrl+V on Windows/Linux). This new option in the NoMachine Connection Menu is intended to allow users to swap Control and Command modifiers, so that users connecting from OS X to Windows/Linux (or vice-versa) can comfortably continue to use some of their local shortcuts also inside the NoMachine session.

It is possible to swap the following :

Win-Mac: Map Ctrl to Cmd and Win to Ctrl 

Mac-Win: Map Cmd to Ctrl and Ctrl to Win

Lin-Mac: Map Ctrl to Cmd and Super to Ctrl

The option can be enabled in the NoMachine session menu, once the user is already connected.

1) Start the connection to the target host
2) Ctrl-Alt-0 to open the NoMachine connection menu
3) Select Input and enable the box 'Map......'

When this option is not enabled, instead, the user has to use the remote modifier for applying keyboard shortcuts inside the NoMachine session.