Theocracity, yes, I prefer my 40k background with patches of light, rather than the darker than dark during an eclipse, at midnight, down the bottom of a coal mine with no torch or matches some people seem to favour, but to be honest, the whole background is a mess of superstition mixed with technical knowhow, there is no real consistency anywhere.
For instance, not even going into BL stuff, the AM are said to have an absolute stranglehold on technology, but the Calidus assassin has to know everything technical (amongst other things), in case they have to take on a role requiring that information in order to get to their target.
And do you think every single freighter travels with an AM adept in the engine room? If they did, aside from it diverting all those adepts from the serious business of contemplating an M8 bolt or whatever it is the AM do, the AM would rival the Administratum for size. It's more likely that the crews do the maintenance themselves (a junior apprenticing to another engineer, then either taking the role or moving to another vessel once they've finished), and the AM run the shipyards for major maintenance (which is normally based around the higher tech items), and give the vessels the equivalent of an MOT every few years, all for a fee.
And all that does is change the fluff from "the AM have a stranglehold on technology" to "the AM have a stranglehold on high technology".
The big vessels exist because they give the economies of scale, plus there's a certain arrogance that humanity can make bigger and tougher things than anyone else, marking them out as the ultimate rulers of the galaxy. I've never said anything otherwise.
The small vessels exist because they fill niches the bigger vessels cannot, or will not, take themselves.