Yeah. The problem is that I get the door upgrade every single time I don't get boarded.
Also, air takes a strangely long amount of time to vent in my experience. This gives boarders time to blow your shield unit, drone control or fire control to stuff, aka the only things keeping you alive, especially with the engi ship.
Depending on which Engi ship variation you're using, theres 2 different strategies that can rape boarders.
With A:
Vent every single room except for Weapons, Shields, Engines, and Bridge. Then upgrade doors, and you'll be set.
With B:
Since you only have 1 crewmember, vent everything except for the bridge, it'll automatically deal with any fires, and your droids already onboard can do any repairing in a vacuum.