Facility increase

Yes, once the atmosphere is breatheable, the domes come down and you can build more facilities.

"Genius is Simplicity" chris connors
"To win without fighting is best" sun tsu
those who think they know everything are annoying to those of us who do

Just click on the construction button when planet is selected, you should see the additional space listed.

Bear in mind though - that requires that you have only that atmosphere's breathers on your planet. If you're an Oxygen race, and settle on a Methane world, and some Hydrogen breathers migrate to that world (thanks to a treaty you have) converting that Methane world to an Oxygen world will not remove the domes. You'd have to go in and remove the Hydrogen breathers.

What if you start the game as an oxygen race, then colonize a hydrogen planet with a methane race, then build an atmospheric modification plant-will the atmosphere convert to oxygen (starting race) or methane (race on planet)?

I think I read in another thread that it converts to the dominant population's preferred atmosphere.