Clearly they are aiming to get all the benefits of the mind flayer tadpoles without having the hosts turn into mindflayers.
The opposite is hinted at in the game.
The Underdark "scholar" tells you that as soon as the stasis gets removed the transformation will be instant. Imo this is the fate Raphael hints at, and also why he is so sure that the PC will be willing to make a deal with him in the end.
Might be a plot similar to some extent to the doppelgangers in BG1.
Edit: I'd also add that the BG games don't have a common theme of 'gods playing with mortals'. Other deities are forbidden from interfering directly in the Bhaalspawn conflict. The common theme is the antagonist trying to achieve godhood.
