the script books for Firefly
, with those roughed out deck plans and cross-sections of the titular cargo freighter, so the suggestions for deck space arrangements make some degree of sense. Your comment about not needing to allow for 21st Century-tech cameras is as likely true as it is devilish!
As to the engineering spaces...you could probably put those on either deck, although a shipwright might
be inclined to have as short a distance as possible for travel between the engine "room" and the cockpit/bridge.
(Need to allow for reactant tankage, storage for crew-consumables, spaces for RCS thrusters, and so forth as well...and you said this baby's expected to be away from the core systems - and anywhere else that's considered "known" - for extended stretches. Up to a year or two? I have got to re-read Buried Age