...Indeed, an industrial installation (a bit like a modern brewery, say) filling most of the engineering hull with multiple parallel and redundant power production units in compact armored casings (looking much like today's reactor vessels or fluid tanks) all pumping power through a central regulating dilithium installation (because the high cost of dilithium precludes individual dilithium foci for each reactor), all normally controlled from a small cluster of "shirtsleeves" monitoring rooms, would make a lot of sense, now wouldn't it...?
As technology evolved, things would get more compact, so each successive refit would free up more internal room in the engineering hull - just like happened to WWI battleships modified for WWII. If one lacked better ideas, one could use the liberated volume for, say, cargo storage.
Timo Saloniemi