It's been a while since I last played the game, but I don't think dying in the fortress affects any of the cutscenes where the Transcendent One kills the companions, right? But the readme does say that it affects the amount of times you can resurrect. Wouldn't a possible solution be to simply remove the cutscenes where the Transcendent One kills your partymembers (if that is possible)?
So assuming you brought only Annah and Dak'kon, dying once would remove either Annah or Dak'kon's death scene (done at random) and leave you with one life and watching the cutscene of whoever didn't die as a result of your previous resurrection. I assume Morte and Vhailor don't count towards the amount of resurrections, since they are an undead and a ghost respectively.
Which leaves Ignus. He could either not have an effect on the count (the Transcendent One simply resurrects him if one of your resurrections claim his life, like he does if you killed him yourself before going to the Fortress) or he could count, which would mean dying could remove him as an obstacle.
I don't think this would require any additional dialogue and the end result is the same (the bodies of your companions being grouped together on the final map).
