In order to deal with an unrealistic, artificial restriction, explain it with an unrealistic, artificial technology that is ubiquitous in science fiction. 99% of TV / movie portrayals of fictional spaceships have artificial gravity on board, because it's just too expensive to simulate zero G on film. (Although there's a feature film being shot in orbit soon...) The large majority of science fiction books also have artificial gravity, because it's generally accepted by audiences and less risky than trying to go hard sci-fi but then messing up the realities of zero-G life. So, assume that your spaceship also has artificial gravity.
Next, specify that the grav plates that create the artificial gravity:
- do not have the gravity diminish in proportion to the square of the distance from the plate, but instead
- perfectly simulate 1G within 3 metres* above the plate but suddenly drop to zero G at a greater distance; and
- plates next to each other do not interfere, but a plate operating above another plate causes catastrophic gravitational effects.
*If you really need a higher ceiling to allow vehicles or (shudder) mechs then you can stretch it to 4m, assuming average-height modern humans, but that height could be split into two levels if there was a shortage of space.
Hence, the occupied part of the ship is at 1G and must be all on one level. There may be fuel tankage occupying other levels, but there is no ability or reason for the crew (or other players) to go there.