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.
Not to mention other things which seem pretty illogical, like why kill the illithids right away if you want to have an illithid army, and why kill your partner immediately as they're also a very strong asset who would help you with your conquest. Not saying the option can't be there, but then the other option (to remain together) should also be available.
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. 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.
I can forgive writing inconsistencies, but I cannot forgive sloppily rushed endings that don't even allow me to roleplay the character properly, especially after making us wait over half a year for... this. I also was going to include the full dialogue of the prophecy with the Echo of [Whichever] from the Tribunal, but unfortunately all my saves are after I killed Orin or in ACT II's Shadowfell. Just didn't have the motivation to go through it, but I might go torture myself even more if it gets Chosen Dark Urge players their proper ending

Thank you again for your dedication and all the amazing work that you do!! If you need the video you can PM me and I'll record it from my save.