I appreciate the intention behind this, and I'm always happy to see folks leveraging the electronics to the fullest. Unfortunate that the complexity messes things up for multiplayer, but that's just the way it goes for now.
From a utility and safety standpoint, it's iffy. To quote a certain engineer, "The more they overthink the plumbing, the easier it is to stop up the drain." Idiot-proofing doors against opening them while flooding sounds nice, but as you've discovered, the problem shows up when you need to re-open the door in order to conduct repairs. No matter what delay you put into place, water will surge through that opening with every button click. What's worse, it's a traitor's or griefer's dream come true: Pluck the system that locks it down and suddenly the door floods the boat moment any player (or creature!) gets close. All that being said, I like it. Use it on big boats, "civilian" ones, or fixed stations. Use it on boats intended for mechanical messes and traitor modes, and it'll be a nice touch.
My only real criticism is the water detection and alerts. The detectors are above the floor so a certain amount of flooding is required. Remember that doors take about a half-second to actually close. As high-pressure water rushes in, you're delaying that closure even longer, allowing more water to rush through. Every second counts when you consider the effect of flooding on ballast. In addition, the buzzers to indicate flooding are a bit excessive and misleading. Sound travels pretty well in Barotrauma, even through closed and flooded compartments. How will you be able to tell which compartment is flooded if there are identical buzzers on the decks immediately above, below, or (in the case of that thin airlock-like shaft) just across? They'll all sound mostly the same, all while drowning out much of everything else. Approaching to check if the door opens means you're totally resting your fate on whether or not the lock down system is working correctly, and if folks previously locked the doors (perhaps because they were standing at a console too close to one, so they forced it shut while in battle), there's no way to know if you're unlocking a flooded compartment or not. I used lights to avoid this problem, and sensors right at the bottom of the floor. Even if they trip at the slightest drip, it's better than opening it by mistake. Submariner etiquette 101 is to keep all compartments closed whenever at battlestations, since you never know when or where a catastrophic breach might occur.
Hope this helps a bit. Keep going!
"I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way."
United Colonies Navy Ship Pack - UPDATED: 28 MAY 18
The Sailor's Manual - UPDATED: 1 JUNE 18