On the whole I agree with a lot of what you're saying, particularly with regards to how starships would more likely be designed with their payloads rather than their hull shape, but I'm going to quibble a bit on one point:
Well there's also the fact that the age-of-sail comparison completely breaks down when you try to extrapolate it into practical technology: smaller vessels made better explorers because they could maneuver effectively in places their larger counterparts couldn't safely travel and could use a wider range of ports (or no port at all) between missions.
It's interesting that Cook chose Whitby Colliers not because they were small, but precisely the opposite reason: They were boxy, had much bigger holds but were shallow draughted vessels. In effect the main problem was that warships simply didn't have a large enough hold for supplies and spares, while colliers didn't have an entire deck made up of guns and could hold a large enough hold.
I suppose it would be like the difference between building a fighter aircraft and an AWACS plane today.
I'd imagine when we're talking starships, the difference becomes that it's just plain easier to load them up with weapons while you're at it in terms of putting in things like sensors and surveying equipment. You don't really pay a penalty for making it bigger (except perhaps for economics) so you're able to build them bigger and better.