Sorry if this is a repeated alert, couldn't find it anywhere else.

I've noticed 2 issues with creating a custom faction both related to population types.

1. When selecting the population collection bonus (10, 20, 50 population) all options refer to the presence of X population type in system. I checked using a horatio-based faction and the UE collection bonus and I get no 15% influence bonus from my own population. Presumably it would work if I collected some UE population but doesn't seem like an intended mechanic from the primary faction population.
2. With the same faction I found that the main quest and also at least one side quest required me to build Horatio population, and the reward is a building which gives bonuses per Horatio (e.g. Cultural Apogee Centre) even when I'm not Horatio.

I suspect it just hasn't been noticed yet,  but it seems like there's a recurring need for some kind of [insert your faction's population] on any quest, building or empire trait based upon your own custom faction.

Hope this helps, loving MP except when it desyncs!