I could imagine that many 'components' are integrated into the hull rather than built modular to be added later on (as Nibelung mentioned). Especially cargo holds - basicly a lot of open space with walls around it - are a good example. You can't exactly prefab an area of open space, can you? While it's possible to build them in a modular system, think containers, it'd save a lot of space to plan them out for each ship individually to increase the available space (by using the integrity of the hull and not needing to build 4 walls a floor and a ceiling for each hold) and reduce costs. Crew quarters could be stacked closer together for 'maintenance' of the atmosphere, water, cantines, etc. where prefabbed they'd each need atmospheric regulation, water reservoirs, a cantine and cooking unit, etc. thereby increasing the costs of each quarter unit. Storing or designing these central systems for each ship/class individually may take longer but is way more effective looking from a real life perspective.