Here's a horribly awkward idea, though I'm not sure it addresses the core concern.
Make Neinzul Combat Carrier some sort of modular hive golem. The module you select determines what youngling it starts storing up/building, up to capacity X. Either give it some sort of smarts, or some "unload" button. Idea being to make it more like the ole minor faction neinzul ships...
Give it some radar dampening, tractor immunity, let it fly up to its target, unload it's entire stockpile. And then die. Give it Neinzul-type build price on a starship-type scale. Like 40K M/C?
Benefit: This would result in a combat carrier just as useful if you unlocked one or all of the bonus ship types. If you had to, you could have more 'carrier modules' on the flanks.
Drawback: Unloading with modules sounds awkward. The concept is solid, but it might be best to hide any sort of modular interface and just toggle on/off unlocked types, splitting capacity between them.
