My idea is to leave your current method of air distribution, but add to it. Leave the "bubble-makers" and add a sort of "room scrubber" where it fills rooms rather than bubbles with air. Also for these two blocks, add another block that would go into the tube network you currently have that allows you to create an atmosphere from air tanks, almost like a furnace, but it doesn't need coal, but you CAN turn it off and on, allowing for player-proof rooms in large scale facilities on servers. Just a few ideas, I have no clue how to code, but some of this doesn't seem too difficult.
