Thanks everyone for the help, this made things a lot easier to sort through.
Christopher Van Horn wrote:
I would point to the last boss of the original kingmaker AP who had levels in Sorcerer and then added levels of mystic theurge using it's inherent caster levels. It follows that these things do stack although as mentioned above class abilities will use the actual levels in the class and not caster level.
Looking at one of the few stated dragons with class levels in Pathfinder, specifically Kazayon, a Great Wyrm Blue Dragon Fighter 1/Eldritch Knight 4, plus Nyrissa (last boss of og Kingmaker) Prestige Classes defiantly stack with inherent caster levels.
On the subject of sorcerer bloodline origins, sometimes it is not that an ancestor was exposed to something, so much as "you," were exposed to something (either long term or sheer potency). Undead with sorcerer levels generally fall under that reasoning to my knowledge.