I suppose it largely depends on your interpretation of things. Are battleships super massive things that require tons of crew? Do they require specialized shipyards, etc?
For your RP excuse of these factions having things... How different are the large transports from the military ships? For a analogy, take the modern world. Big tankers could be a bit up armored and given weapons. Do they? Obviously not, but when the weapons themselves and the ammo aren't to much of a concern... They could, technically.
So in the decentralized realm of Sirus, why not have low key people have capital ships? Not a lot, of course, but some.
Even if things don't make technical sense, it's been, what, twenty years since the actual storyline? Things change! Change them, adjust things to make it work. Hordes of samey fighters aren't as fun as accenting those hordes of samey fighters with some bigger things.
Why not?
But.
I do think they should be player-faction only things, as both a incentive for people to join up together and to keep people from trippin' caps.