I guess you could use any shuttlecraft as an analogue. They all have the various systems you describe, even the TOS versions, and they all seem to somehow fit it into a volume scarcely larger than the shuttle itself. Heck, even cloaking devices can be fit into an oversize suitcase if you had to do it.
The base conclusion we have to reach is that all the hardware is already tiny by our standards and thus doesn't take up THAT much space. Indeed, we hardly see ANY of the major hardware on a full-size starship save for a warp core and sometimes the computer core. I'm guessing pretty much everything save tanks for fuel and water would not take up any significant space in the Trek universe unless specifically shown as such.