The "passenger train" idea is an interesting one, but I think the ship would be a little wider than that. What I'm imagining is that it's wide enough for a narrow corridor with compact, maybe Defiant-sized staterooms on either side, but that areas like the lounge and lab would be pretty much full-width. So in the deck-1 plan I'm imagining, you'd have the bridge/cockpit in front, then maybe a short corridor with storage space and a stairway down, then a door leading into the lab area, and then behind the lab would be the medical bay on one side and the transporter stage on the other with an open passage between them, leading to an open area in back with engineering consoles and maintenance access as well as storage. Maybe a second stairway coming up next to the medical bay. And then below you'd have the nav deflector and sensors taking up the forward space, then the bottom of the stairway, then a corridor with quarters on either side, and behind that the lounge/mess area and the head, then cargo storage behind that.
On the lifeboat question: could the staterooms themselves double as lifeboats? I think that would save space.
As someone who's lived in a walkup apartment, I would suggest adding some sort of lift or service elevator. Something they can use to move equipment and other heavy things between decks, without having to use the transporter or trying to negotiate the stairways with heavy loads.
As for quarters doubling as pods, they'd need redundant and effective safeguards against accidental (or otherwise premature) launch. There might arguably also be drawbacks to keeping pod power and fuel sources structurally linked to quarters in everyday use, but that would probably depend on the actual design.