[Q]

I just ran a small test to see what happens, if a race that lives in no athmosphere uses an athmospheric modification plant on a Gas Giant:

Nothing happens at all! The athmosphere will simply not be changed.

Of course a Gas Giant with no athmosphere would be a little bit strange, but I think this is quite a severe handicap for a player who choses no athmosphere on the home planet. Especially for the AI who does not use foreign races to colonize non breathebel planets in contrast to the human players.