I've been going through the available factions, looking just how many points short or over some of them are, and Horatio doesn't seem to have its food bonus - nor is a +3 available. 

Is that a relic from before a bonus was nerfed?

Or does it somehow stack two bonuses, which a custom faction can not?

Alas you can not exactly replicate the Horatio's base population as there are no +3 Food primary buffs but rather +5, +2 and +1. Therefore the primary is unique or a combination of the latter two primary Food buffs. Besides, if you're looking to make a custom Horatio, there are better options: Adept Workers(+5 IDS, becomes +10 when boosted unless Riftborn affinity. Add a secondary Food and you got one wicked Population), Meritocratic(+2 FIDSI, custom UE works great with this since you get +4 of everything when boosted. Add secondary of your choice like Hardened Dwellers for +3 Loyalty on Sterile), or Extreme Foremen(+150% FIDS output, +1 Depletion). Extreme Foremen or the Cravers primary buff can be insanely OP with a Gene Hunter or Horatio affinity since you can offset the malus with Planet Menders secondary and Sowers starting Minor Population(which removes the malus when assimilated).

Yeh, I tried that just for giggles recently. Primary system reached 130k Industry. That's not really my aim, though - I just wondered how things would have to be priced to be balanced, given that the base factions (which I assume at least somewhat balanced) seem to vary between 70 and 135 points. 
Turns out it's hard to tell at times.