I don't think this is a plot hole, and with dnd, in Faerun, the rules and lore can sometimes get muddle. For example there are occasionally Good Aligned Demons or Devils which lore-wise should be nigh impossible. Therefor, it isn't out of the question that a Vampire Spawn could still have their soul, possibly due to the machinations of their lord, in this case Salazar. In fact it is possible Salazar currently has his soul cause that makes it easier to puppet his Thralls and the reason he doesn't destroy it is cause Astarion is his favorite plaything. With this it wouldn't be impossible that the deal Astarion could make is something along the lines of "When your soul is released from the clutches of your Master it will transfer to Raphael." This would fit the conflict of him possibly having to go from one horrid slavedriver to another.
