I hope you throw in a "vent the oxygen" feature to help repel boarders/invaders. Even if it doesn't make a hell of a lot of sense (surely they've got space suits), it was always fun in FTL and promoted a certain amount of evil cackling.
Maybe acid and poison spray options as well, for the better equipped/suited or more resilient attackers, with cleanup costs or deterioration of the room that you just filled full of evil afterwards.
Even if it was just an air venting option, it would be nice if there was some risk involved. Rather than an entire door-system level that was 100% reliable and ship/colony-wide, have individual bulkheads as components. Some with high resistance to melee/breeching, some to venting procedures, some to chemical attack, and some all-rounders. That way, when you do vent a room, there's a chance of the surrounding bulkheads buckling or being compromised by toxins, potentially creating a catastrophic chain reaction of accidentally venting/flooding half of your ship/colony when you only wanted to do one room. If repairs were necessary to seal air/toxin breaches during/after this, it would make you really think about if you wanted to simply fight them or just suffocate them. It would also give another dimension to ship/colony and room design with the consummate parts required for the different types of doors and the venting/flooding procedures available to you, giving a bit of a DF "trap room" feel to some parts of the colony. As well as varying hazmat suits available as equipment options for some crew members as another "job type" for them to do, to deal with the (un)intended catastrophes resulting from this.
If you do add a bit of a temperature/radiation system on top of that, you'd have a very satisfying system for setting up defenses that didn't require guns, but with pitfalls, costs and risks involved to it. Set a reactor to sub-critical-overload to flood a room or five with radiation? Even if it'll tick up to "over-critical mega-death-explosion" if you do, and you've got no radiation hazmat suits to deal with it? Sure! If the threat is big enough. You'll still have to send someone in there to fix it anyway, and as they say, "The needs of the many outweigh the needs of the few, and we ran out of redshirts two sectors ago......"
The bulkheads could be pretty reliable (65-98%), depending on the venting/contamination that they're securing, but we all know how often you can fail 2/3rd chance rolls in a row sometimes. Maybe even just have a "standard" door level ship/colony-wide, but with upgraded individual doors available to set up things like this. Depends on how you want to do progression and itemization in the game. Some rooms could even have decontamination bonuses, so door breaches are harder or can lower the damage around them by a large percent. Bio-lab near/in a toxin trap room? No biggy, that's half the reason you've got toxin traps in the first place
You could even fill a room full of acid spray to eat through their suits/armour, wait a bit, *then* vent some rooms, ensuring suffocation to the well equipped/suited intruders invading your ship. While hoping the acid doesn't start to eat through your science lab next door, during or after the attack. At worst, you've made their armour crappy and caused a few little (big?) problems and costs for yourself. At best, you've got a maniacal grin on your face due to your evil genius in ship/colony planning while you watch your enemies die in agony. It might have cost you some of your acid spray, and putting a crappy non-combat hazmat suit on someone, but it's priceless.
Of course, it goes the other way too:
"Sorry Cap! We killed all the invaders, but now half the colony is full of poison gas. I told ya the doors needed upgrading!"