I would work on your evasion and stealth. Damage control works just fine for me, I don't even click anything, it all happens automatically. I would guess that any available intervention on behalf of the player (more crew to damage control/flooding, clicking on subsystems to prioritize repairs) has a very narrow window of overall damage to be considered effective. Meaning, the way the mod author envisioned this damage model was to make it more realistic in that those interactions are for helping a damaged ship, but not a "magic" repair to a doomed vessel, as in the un-modded game.
In my experience certain zones are more fragile than others in the boat. You are either extremely unlucky and these areas are getting hit all the time, or you are being reckless. Or perhaps you are just testing getting damaged for a future career/campaign?
If I'm sinking by the bow, emergency reverse has brought me to the surface. The opposite applies when sinking astern. Of course none of this is possible if your engines have been knocked out.
Good luck!
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