If I've understood correctly, a sector is like a map from e.g. galciv3. So a small sector would be the approximate size of a small galciv 3 map and a large sector would be the approximate size of a large galciv3 map.
I think the player should be able to customise their starting sector start as much as possible. I agree with Larsenex that there should be a maximum number of civs per sector depending on size. So for example a small sector would have a maximum of 2 or 3 civs and a large sector would have a maximum of 5 or 6 civs. RNG would determine the actual number of starting civs in any given sector. So for example in a large sector there's a chance that no other civ spawns, or only 1 civ spawns or the maximum number of civs spawn or any number inbetween.
I also think that if the player doesn't want to be at the mercy of the RNG they should be able to choose how many civs start in their sector. If they want to be the only civ that starts in their sector then they should be able to select 0. If they want the maximum number of civs for their chosen sector size then they should be able to select whatever that number is.
This would probably be helpful for modding as well e.g. if u wanted to make a Star Trek mod you'd want to be able to select how many civs start in any given sector. I'm sure Star Trek modders would love to be able to create the actual Star Trek map in galciv4 with all the factions in their correct starting positions.
I also agree with Larsenex's other suggestion of being able to choose the minimum spawning distance of other civs to the player's capital.