On general damage control and such. Warships would have more of this than merchant ships, cost being far less of an issue with the former. Besides, merchant ships generally aren't going to be designed for combat.
Some things I'd suggest as design features:
All redundant systems are duplicated such that they run on opposite sides of the ship. That is, the normal feed is on one side, the alternate is on the other.
The fuel tanks would have to be something like thermos bottles and I'd surround those with a separate compartment (it wouldn't have to be very wide) that is either normally in vacuum or was filled with an inert gas like argon or nitrogen. That makes it harder for one to leak such that it does into a space that makes a risk of fire very low.
Venting fuel overboard would be possible to do. Shifting fuel out of one tank to another would also be doable.
There'd be lots of fuel tanks rather than one or a few large one(s).
All bulkhead penetrations would be airtight going through well designed stuffing tubes that would minimize the risk of fire getting through that way and prevent loss of atmosphere between compartments. Something like this:
These would be a standard part you could order so some variant would be used on any ship by any constructor.
Not all walls or floors on a ship are bulkheads or decks. Some are partitions (thin walls not intended to stop fire or loss of atmosphere) and platforms. These have doors not hatches.
Use of finishes and materials that are fireproof would be common.
There is emergency lighting and you have to change the batteries or it doesn't work when you need it. It doesn't magically work when the power goes away because you still need something to power it.
Water and waste disposal are normally centralized systems because it saves a lot of space and weight over having it decentralized. It also means you can recycle the water and whatnot easier. In other words, the ship has one or more septic (called CHT on ships) tanks for sewage. You just fire the contents overboard somewhere convenient in space and hope it doesn't turn into a "blue asteroid..."
Hydraulic systems are fine. The fluid would be something non-flammable. They work well for giving a lot of umpf in a compact system.
Pneumatics would be similar. You use an inert gas if the system is closed loop.
For example, rotating all those turrets is best done with a local hydraulic system as you can get anything from very high rates of rotation to very fine slow ones and these are very smooth. You could also have one system driving multiple turrets at the same time.
The fuel processing plant(s) need to be isolated spaces due to what you're doing in them. Placing these in an engine room or elsewhere with other "stuff" only increases the danger during making fuel.
On hatches, most are not automatic on my ships. You have to manually operate them. Having the sort you see in sci fi movies all the time would be a maintenance nightmare. The tracks for the sliding sort would get stuff in them. You have to find room in partitions and bulkheads for them to move into. Instead, they're simply operated with a hand wheel most of the time.
Something more like this:
The sort of iris valve ones would be another maintenance nightmare. Could you imagine trying to keep all the surfaces clean and nice and smooth over say 20 years? Plus they have the slide into the bulkhead issue to contend with.
Instead, the hatch operates like a door and the dogs to seal it are contained inside a panel on the door. If it's automatic you have the motor and such in the door panel and just wiring from it to the ship. The seal around the door and the bulkhead knife edge are easy to clean and maintain.
Yes, you have to step over the hatch combing...
For those inane hand wheel sort of deck hatches you could use something like this:
That T-wrench would be nearby... At least until it magically disappears and needs replacement right when you need it to operate the hatch...
On engine rooms... IMTU these are noisy, hot, and filled with stuff that you shouldn't brush up against. There's very little open space in them (the antithesis of
Star Trek engine rooms). Why waste space in them that could be applied to other things like more cargo?