Having two x2 stack into a x3 still doesn't feel right IMO. Doing the Tweraif ending is practically just busywork after successfully grabbing and returning with the veil, and isn't really comparable to taking on Petrus for the chaos ending. Adding a static bonus score X for completing a quest seems more in line to me with the multiplier only being determined by the ending you get.
Static bonus seems like the best option. Either that or add the square root of the subsequent victory score.
IMHO the mutual exclusivity of the various quests is kind of lame. I dont like how you cant do both. why can the high priest of petrus then go kick the asses of the armies of chaos?
But what would be the victory condition after the high priest victory? Do we register the score at that point and stop counting, or keep adding to the score?
After all the quests have been achieved, I guess the only thing left would be for the character to die. That would definitely be in keeping with the game