Well, all that's to say: I don't find such inconsistencies all that important when there's a bigger, glaring issue with these endings, in my opinion. A lot of this stuff you can handwave away pretty easily "Sceleritas was lying" "Her prophecy was just poetry" etc etc. It doesn't seem the craziest thing to me that a Chosen of Bhaal wouldn't want to create more life (as Sceleritas so... succintly describes) rather than ending it for everyone.
That's ok if you think so. For me it's a huge problem regarding player agency as Crimsomrider already described very well. I strongly feel there should be at least one option where you can still be together with your partner. Instead we get 3 options where you're pigeonholed into not being allowed that, no matter your roleplay choices beforehand.
I believe that can happen regardless of if you're the DU or not, as long as you become the Unholy Assassin. And then, even as the DU (if you don't embrace Bhaal) you could also just choose /not/ to conquer the brain, thus having the prophecy be possible.
EDIT: My bad, while you do need to become the assassin, her question is locked behind the flag that you're the DU. But you could still choose not to embrace Bhaal afterwards, I think?
Except there's the last part of her prophecy, where she says after your deaths, Bhaal will come to collect. But yeah the part about dying together at the end of days could otherwise still be possible as a redeemed Dark Urge... Though in that case, you're not likely to hear the prophecy in the first place, if at all.