I'll need to look into this, not sure what remapping does to the incoming key events.
Also I'm already working on a ui for customizing the key bindings so you could do whatever you wanted. (Currently managed by undocumented json)
Thanks for reporting!
This is probably not your responsibility. Modifier keys and especially rebinding them are really in the realm of the OS and the Terminal emulator. The application really shouldn't have to do special things to accommodate Mac OS idiosyncrasies.