[Andrés]

Mainly, reality is much more complex than SE4, and it seems to me from considering real-world examples, that one of the constants is that bigger is almost universally more expensive per unit measure rather than less - it's up to the larger and more expensive designs to realize their worth through even better performance.

I don't know where you get that impression from.
I think you may be comparing a group of tiny ships that is actually smaller than the massive one. If they are enough for the job, then yes the big ship would be overkill, but that does not make it less efficient.
That logic does not make any sense.
In general bigger designs are more efficient BECAUSE they are bigger.
Buying a large bottle of Coke is cheaper than buying many small cans.
Installing central air conditioning in a building is cheaper than installing an individual unit in every room (specially when it comes to usage and mantenance cost)
The same goes for ship systems.
Building a heavy baseship must be much cheaper than an equivalent tonnage of frigates.
Frigates will have their advantages, harder to hit, can be built faster by using many SYs. When it comes to use they can be much more flexibe being able to operate in many places at once.
Heavy baseships advantage is only being cheaper and more efficient.
Yes there are many technical details such as specialized parts, facilities, and support know how and technologies.
That is what's why you have to research to get larger hull, anyone that can design a certain ship can easily design something twice as big, research means solving all those technical issues involved in the larger design.