This is just a thought, but perhaps i am misunderstanding the question: if you take all your frigates and put them on page 0, and all the cruisers on page one, then they will still be in the same "factory" but you will have a page dedicated to each type of ship.
I tried adding a second frigate factory, but since the player entity file itself doesnt separate out the entries, and wont take second listings, (i think i would get a mini-dump) that it wont properly give us a second useable frigate factory.
As mentioned above though, creating a second factory though, that "spawns" the cruisiers, is something that can be done. Look at the combat turrets and how they are spawned for reference, or look at some mods on the forum where people have done this.
My own StarFall mod does this.
It was a huge pain to learn, haha, but now that its figured out, it seems fairly straight forward, go figure, haha, anyway, good luck and let us know how it works out. If you need help, just ask.