I think this is just a simple balancing act. The idea is that some factions need more than just a few generals and if they would be part of the family tree, the family would grow too fast as the growth is sort of exponential. So you get some generals to start with who will not "bloat" your family too fast later on. Later the situation is easily fixed.

It seems that there is no real limit on the amount of family you can have, as I have a general for 80% of my settlements plus a few warring generals and as the english, I control the british isles and the old territories of france.