Modular main chamber + navigation + hygeine + likely very small personal chambers + growing chamber.
A common mistake is that people try to treat colony ships like flying houses or skyscrapers. A closer (but still not quite there comparison) is an early colony sailing ship with the realization that it doesn't have a world to support it.
Most boats had a main room and a main deck for daily activities depending on whether the weather was nice enough to be inside and outside. It's hard vacuum outside, so the purpose of two main areas is removed, leaving only one. Navigation needs to be seperate purely so day-to-day activities don't interfere with navigation consoles. Since a lot would be automated, probably doesn't need to be very big, but you'd want it because in an emergency, you want to have manual controls if modifying flight plans on a tablet is unworkable for some reason (like power outage). Personal rooms are needed because people snore and they want to store their personal possessions. Depending on space requirements, these may be only a personal locker, and a seperate set of enclosed bunk areas that people switch out of. Otherwise, the main area would likely be adapted to whatever needs are currently needed. People want privacy when on the privvy and you don't want stuff flying around, so they'd probably be seperate. As for growing, plants are kinda messy (parts break off, wilt, decompose, drop fruit, there's juices, etc.) and have special needs (lots of light panels, hydration, nutrients, all automated as much as possible).
Additional potential "messy"/specialty rooms that may warrent their own compartments depending on size of ship:
- red light area
- emergency response equipment (medical, hull breaches, fires, etc.), likely placed near center of hub for fast access
- chemical processing
- 3D printing enclosures
Also worth noting that these are just physical containers. As incorporating VR, AR, into the structure is highly likely due to it's benefits of space efficiency, VR spaces are likely to constantly be created for various purposes (and may or may not have dedicated space for those using them, possibly incorporated into personal spaces).