Can't find any undead with possession ability. Are you sure it's and undead creature you want to cast out of another's body? May be it's an outsider?
If an undead caster invades a living body with Magic Jar, i would say he will share that creature's abilities, creature type, weaknesses, and immunity to Command Undead feat.
Possession rules in Occult Adventures let you target a possessing entity with mind-affecting if you know the target is possessed. I'd treat it the same for Command Undead and let it work.