[@Terminal]Per case basis allowances to the rules sounds like a good solution.
As for sizes, they kinda also represent the industrial power of a nation.
So a more primitive nation should have inferior industry thus:
A.) Even though the 12-mile ships are classified as destroyers, they aren't nearly as numerous as the common ships of the other
B.) There are other technical details which makes the creation of larger ships difficult, maintaining a stable field for FTL travel, for example.

Such discrepancies will be occurring regularly within the RP. There's no way to completely mend them aside from invasive intervention from the GM, which isn't really advisable.