For all we know the Flagship doesn't follow the normal standards. I mean it can spit over 6 drones at you at any given time and also shoot lasers out like if the game was in alpha. (long time ago weapons are not visible and you just got projectiles shooting from the centre). The Flagship also has the ability to automatically get a super shield up without an FTL jump or the new shield drone.
The hacking system is just like everyone else's no matter what the ship. Just because it has a few tricks doesn't mean it disobeys all the rules. The Cloak after all lasts only 15 seconds, not 5 years as I think it does.
I remember hacking enemies with higher level O2's and it draining as fast as if like they had all there doors open with a breach. I am not sure if they hack my O2 as I never run 3 bars when I know it's already hacked. I run 3 bars between the charge times so then I can regen what I lost. That and in a normal situation in combat I run 3 to boost my O2 and then let it at 1 when I am at max.
Medbay and O2 hacks are set amounts of drain/damage regardless of system level. I know this because I'm terrible at power micromanagement. I'm the sort of person who buys a Backup Battery and never uses it.
If my O2 gets hacked, I tend to leave it on two bars and that's enough to mitigate the loss from hacking.
Oh right, I think I'm supposed to talk about the ship.
I'm not a big fan of oxygenless ships unless it's a Lanius vessel or has Ghosts.
This is no exception. What kind of crew would willingly put themselves in such a deathtrap (and constantly too)
I mean the Asylum made sense as it was full of insane Zoltans.