The two main factions seem good but alliances could allow multiple companys to work together with similar settings to company ships and the ability to align yourself with Empire/Kingdom if either faction thinks your company/alliance meets their standards and morals.
Base locations is tough because while i have my bias already that doesnt change much here both factions need to be in a good position to be able to in general play the game but likely also built to see combat and launch a lot of fighters or larger ships so they'd have to be somewhat equal in their HQ locations.
a contested third station would be a good idea to be sieged at regular intervals perhaps giving control over the gate in some way or just providing a strategic/economic advantage, imagine being able to charge tax or change the safezone size, the point is that the faction gets to make SOME decisions to affect a region they control, I would expect the two factions to have pretty standard behavior with these periods of occupation, Battling it out for their HQ's could also provide some negatives while i don't think a faction should be able to permanently lose their HQ i do think it getting destroyed or "defeated" could simply deny them acess to that station for x amount of days and perhaps any additional benefits it provided for the region/faction.
all in all i failed to answer your question OP as i have literally no idea where they should go lol.