I am pretty sure that it mods to those that inhabits the planet. I have three different races, and the converter seems to change to whatever race is there at the time. Of course, I have limited experience in the game (first universe), so take this with a grain of salt.
It mods it to the race that has the majority on the planet, so if you had different atmos. than the captured race you would need to do a little transporting if you wanted a captured planet to breath your air.