So not to be a debby downer, but I think the freighters need a bit of a nerf.
I have 10+ different ship sets installed, and Foundation freighters generally surpass the very largest modded freighters by a significant margin (40-50% larger cargo than the next largest one in the class). And that's keeping in mind these modded freighters are already a lot better than vanilla ones in the first place.
As far as I can tell, it's not like Foundation freighters have any weakness to offset this (very high maintenance costs, fuel consumption, CR deployment, or combat fragility). In fact, some of them tend to be even more powerful in combat than some combat freighters, which normally have especially low cargo to offset their increased firepower. I know it's not my place to tell you how to write your own mods... but for the sake of balance, I would at least consider adding some sort of drawback if they're going to be so much better than everyone else's ships.