...An important thing to consider is that this overhead space also appears to have to include wiring/cabling, heating/ventilation & air conditioning, fresh and waste water plumbing, and water reclamation and air scrubber equipment, plus grav plates, general structure, and the machinery and space allowances around any deck mounted iris valves etc so there may not be as much space as you might think.
Of course. Only a fraction is available - but you only need a fraction. Consider that ship design only gives us the 4dT stateroom allowance for habitable space. Let's say that 20% overhead is machine space: each 4dT stateroom includes 0.8 dT of machinery overhead and underfoot. Some of that is the grav and inertial damper system, some of it's life support including air recycling, water and water recycling, a solid waste system for the toilets, and so forth, and so forth. Quite a bit of work for that 0.8dT - as well it should be: much of that Cr500 thousand we're spending on a stateroom is bound up in that equipment, at least in CT. (MT makes us pay Cr400,000 for the stateroom but bills us separately for gravitics, inertial dampers and life support, which means that plumbing system must be gold-plated.

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That means each stateroom constitutes 3.2 dT of open space to keep fresh. I compress hydrogen about 800 times to get from the gas to the liquid. If I compress the O2/N2 atmosphere mix only 200 times, then I can fit enough gas to fill that volume in a container of 0.016 dT. I can do that six times and only take up 1/8 the machinery space volume. Modern scuba gear reaches pressures in that range and more, so I can actually store 6 or more "fill-ups" in no more than 1/8 the available overhead space using modern tech.
To me, its the lack of airlocks that really seem to be a big issue. Looking at the following image of a Scout from the images section of this forum as an example, although there are iris valves separating the Bridge from the passageway aft of it, the living spaces, the passageway in way of the cargo space and the machinery spaces etc, the loss of pressurization in way of the cargo bay could lead to no way of getting from the machinery spaces to the Bridge without depressurizing some fairly large space unless you have some sort of "portable airlock' that could be used, but this then presents the question of where those would need to be located and how many are carried and how much space they take up etc.
Beyond this there are also the impact there may be on any systems that passed through the cargo bay and connected passage that may be impacted by the loss of pressurization, power and/or other factors in way of these spaces. ...
If I understand you correctly, you're saying that, because the ship's sections are stacked in a line - bridge/hall/quarters/hall/engine room - a loss of pressure in one of the intermediate compartments cuts the bridge off from the engine room. The crew would have to use one of the compartments as an improvised air lock, and that could have unhappy effects on other items in the compartment being used. Which is where I say the game master can step in and come up with some kind of equipment that serves as an emergency airlock - if that's what he wants in his world.
You need a means of creating a small improvised half-dTon compartment around the iris port - something that will hold tight to the wall around the iris port and that can be depressurized without collapsing. The existence of the pressure tent and the survival bubble both show that there are plastics that can be constructed to hold up under pressure, so imagining a collapsible emergency airlock that can be stored adjacent to the iris valve as standard emergency equipment is not a great hurdle.
... To me, a concept like emergency power for each subsection of a ship would suggest some form of battery power, capacitors(?) or other power generation or storage systems in each section that would need to be placed somewhere. ...
That, or solar panels as standard equipment on the hull. Or both. CT offers no guidance that I know of, but in MegaTrav the basic life support's 0.001 Mw per kiloliter of hull: 0.054 Mw for the typical stateroom allocation. MegaTrav solar panels are - magical, producing several times more power than the sun puts out, but even putting MegaTrav aside and restricting ourselves to the solar output at Earth as a standard, a 6m by 6m panel will power live support for a stateroom. Alternately, 100 kg of TL9 batteries will power life support in the standard stateroom allocation for an hour at a cost of 375 credits. Batteries for 24 hours life support are 2.4 tons (~0.18 dTons) and cost Cr9000. There are better batteries, but they get expensive: the same batteries at TL14 cost 13 times as much but would give you almost a week of life support. (Considering the cost of a stateroom, it'd be nice if we could get something more for it than silk sheets and a flat-screen TV.

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So far I can provide reserve atmosphere and 24-hour life support at TL9 and still have 2/3 of the overhead space available for other equipment. That should at least hold you together until the rescue ship arrives - unless you're too far from rescue.
...To me, the biggest impact that I would see on ship design if the intent were to be to allow damaged sections of the ship to be segregated off from the rest of the ship, then I'd probably expect to see (at the very minimum) would be either to break the ship into discrete sections with either built in air locks between them or specific locations identified for where portable airlocks can be emplaced, plus storage locations for these devices, as well as some thought given for laying out the ship to prevent the loss of any one section of the ship from impacting access to other major sections of the ship...
I've discussed airlock options. Smaller ships, there's a limit to how many different routes can be planned within the limits of the tonnage allocated for habitation. Scouts and free traders and such are just going to have to accept a certain amount of impaired functionality. There's just not a lot of room to play with: the guys are just going to have to get in vacc suits and say goodbye to the wine and the cologne.
...On the topic of the Scout layout I noted above, another issue that likely would need to be addressed is just simple issues like freshers. Although no specific freshers are shown in the deckplan, it appears that enough space is allowed for in the living spaces to allow for fitting them into each stateroom.
However, in looking at the deckplan it does not appear that there is really any other spaces where a fresher may likely be fitted. As such, from the limited data available I'm left wondering if the loss of pressurization in way of the living spaces would mean that the ship is left without any accessible fresher facilities, not to mention food and other such stuff as well.
Freshers are in the stateroom proper. The deck layout's just to show you where things are generally, not to give you details. You also don't see a kitchen, pantry, laundry facilities, closets and so forth. If you want things to that detail, you take the existing deckplan and play around with it.
However, yes, the loss of pressure in the living compartment is a major headache, especially on a ship with only one living compartment (the Subsidized Merchant has two; the Free Trader and Far Trader have living quarters on two decks). You could lose access to your kitchen, your freshers, and so forth. You could find yourself finishing out the voyage living on emergency rations and whatever dried foods survived the incident, and doing your business in chamberpots.
... in the end if the intent is to have a 'saferoom' onboard where the crew could evacuate to in the event of an emergency then I'd suspect that such a space would have to be shown on the ship, complete with maybe emergency fresher spaces and food storage etc (or as an alternative maybe a fresher and emergency food storage facilities should be located in each major hull subdivision.
If you design a dedicated stateroom, yes. I don't like the dedicated stateroom: it's as likely to get hit during battle or from whatever random event strikes as any other section of the ship - as I mentioned. I prefer the idea that ANY section of the ship should be able to serve as an emergency retreat - and an emergency retreat only needs to keep people alive, not make them comfortable. If you have to sleep on the floor of the engine room, go hungry for a few days and poop in the corner to survive, then you sleep on the floor of the engine room, go hungry for a few days and poop in the corner to survive. The important thing is to keep breathing - that, and some emergency water stored here and there; you can go maybe 3 weeks without food, no more than 3 days without water. If you really can't abide pooping in the corner, then a urinal bottle, a bedpan, a lidded barrel with maybe some chemicals at the bottom to contain the stuff and kill some of the odor, and an improvised curtain for privacy will see you through the emergency. Emergencies by their nature are uncomfortable affairs.