First off, I believe the Nova Engine reserves some of the slots for ships in a system for planetary domination simply for that reason. No longer can one swamp the system to force planets to send one ship at a time.
Second, you could just as easily lower the occurrence of carriers showing up. Reinforcement fleets could still be led by carriers, but maybe they won't show up in various systems as much anymore, bar the Fed përs flagships. Carriers are big ships with a price to match. Space-age carriers might would only be bigger. It makes sense to me they wouldn't be mass-produced if given the power they should have in a balancing plug-in; too cost-prohibitive.
Third, doing the Fed string only nets you two kinds of bays: the Viper bay and the Anaconda bay. The Auroran string has the same limit with the Firebird and Phoenix. Sure, you could capture a ship variant with other bays (are there even any like that for the Feds?) but you could simply keep the fighters for those bay variants non-purchasable in terms of outfits. You could even go so far as to eliminate bay variants and have only one navalized variant of each class of fighter. It makes more sense to me, anyway, that military regulations would require standard fighters in service onboard warships, not modified ones that might be less effective in combat or more expensive to maintain.