There is a hard cap of 31 factions (including pope , rebels, emergent) per campaign, you can have seperate campaigns with different factions though but it means for any campaign you start the limit is 31.
The Almoravids and Almohads only co-existed briefly. the later overthrew the former, it was kind of like the Cumans taking over the Pecheng only the head changed but the alliances stayed largely the same. of course there was a string of Almoravids that ran around into the Balerics and later Tunisia that lasted longer but that kinda count as rebels.
In 1100 the Seljuq control outside of modern day Iran is debatable (and even in southern iran). the turkish situation in most of the medieval era was vastly complex, unfortunately you need a ton of faction slots to make that look even remotely reasonable. the engine's greatest limitation is the difficulty in depicting a civil war like faction. like the Kievan Rus or the Turks , they're all loosely part of a same faction, but individually all held their own powers as well.
Anyway. here's my on going attempt to try and push it closer to history. though the limitations can only be compremised so much.