Factions are a way of giving guild permissions more granularity, giving a group of guild members different permissions from another group, you use factions. Why would a faction need to be separated from the main guild?
And as for the original questions I’ll try to explain what I’ve noticed. It doesn’t matter if you align a beacon to the main guild or a faction, they still count as the same guild settlement. Guild settlements are simply a way of easy permission controls and protecting your settlement name from prestige takeovers.
The guild member cap is 100 + 400 gc members across all factions and the main guild. The way it worked was that each faction had their own member limit, but
Fixed guild membership limit workaround using factions.
sounds like it’s not like that anymore.
I’m not 100% sure about buffs since I haven’t played with them myself. What I can say is that one of my characters is in Ultima main guild, the others are in Ultima extended faction but all of them are still getting guild buffs from the main guild since you can set the main guild as your main guild even if you’re a faction member. So you get buffs from the guild you set as your main.