The leaders will nearly always choose a historical civ if they can. The only way this doesn't happen is if (1) you pick their associated Civ first (2) there are multiple leaders vying for the same Civ.
The thing is that most leaders have more than one 'historical choice'.
For instance, Augustus is not guaranteed to get Rome because Rome is the default Civ for basically every western leader, which means he'll often end up as Egypt, which is his other 'historical' civ.
Hatshepsut and Amina are the two leaders for Egypt and Askum. USUALLY it's hatty for egypt and mina for aksum, but sometimes it's the other way around (or one of them as Carthage).
Harriet Tubman and Benjamin Franklin both default to America in Modern, but if both are in the game, one of them will lead a different Civ. (Tubman normally takes Buganda and Franklin Great Britain in those cases)
But for the most part? yeah, Isabella will always pick Spain in Exploration, Ibn Battuta will always lead Abbasids, Himiko will always pick Meiji Japan, Tecumseh will always lead Shawnee, etc, as long as you didn't pick those Civs yourself.