1) Players can count for as many factions as they actively participate in RP for. For instance, if a player plays in a Star Army of Yamatai RP, and in a Nepleslian RP, they count for both. Whether or not factions are in an alliance doesn't affect player count.
2) You do not need to use time guidelines for things that are already built.
3) For each player, you can claim one system - if some players leave, we usually don't force the faction to shrink. The idea is to control the amount of systems that are claimed (each has a maintenance cost and people who add tons of systems don't tend to add very interesting or detailed systems so you end up with these wiki articles that are nothing but blocks of stats), and to make sure that factions with a handful of players can't easily overrun the ones that people are actually actively RPing in (a minority group of players shouldn't be able to easily just topple the majority because stability is important to grow plots on, so to speak).
4. If the faction is an alliance and vice versa, it could be represented as one entity. Otherwise, the factions would be listed separately. For example Elysia is part of Yamatai but it flies its own flag on the map. We can work with people's preferences.