I handle some of the problem with a magical handwave. All interior spaces are squared and level inside the outer hall, with fuel tankage filling all the nooks and crannies. It makes like a lot easier when drawing up deck plans and if the interior space cannot be fully contained within the fuel tanks, I then add small ship hangars inside the outer hull, to fill out that space. Of course this works best with spherical hulls but even wedges have most of the interior spaces square and level, with all the odd spaces used as part of the fuel storage systems. This also allows me to use the same insulation that keeps the fuel at the right temperature, also being used to insulate the interior spaces.
When laying out the actual floorplan, I usually allow 1 ton of displacement=3 meters cubed. This allows me to adjust some of the interior spaces so that a bed doesn't look like it is 3 meters long when about 175 centimeters should be enough. That and a actual height per space of 2.2 meters high, .3 meters in a suspended ceiling hiding ductworks, cabling, etc., with the remainder used as part of the public spaces like corridors, commons, etc.. Of course I usually make the dining room the commons, making it handle double or triple duty.