As an aside, I realize as I write this; was it ever really explained why our companions and Tav remained in total control when we first awakened? The assumption seems to be that we were going to moonrise in order to be fully "turned" but that doesn't actually make sense. We're already tadpoled. The tadpoles control and influence minds. If they've been changed and augmented, wouldn't it make sense that they would immediately bring their hosts under control? It doesn't really make sense that we get tadpoled, but have to be brought to moonrise for the control to "take" does it?
My theory on this is that the Emperor is the one who tadpoled us. The Emperor was known to be in charge of the Nautiloid. We find this out from a book in the Vault.
(Some people say it wasn't the Emperor who tadpoled us because the eye color is different. I say it was and that visual differences are the result of changes made after the intro was put together. For instance, Lae'zel and her armor look completely different in that scene.)
Anyway. The idea is that the Emperor was freed once he was in proximity to the artifact. At that point, he rushed to come up with a plan to fight against the Absolute. He began snatching up people left and right so that he could tadpole them and build up his own opposition. The githyanki appeared in the middle of his plans because they were searching for the stolen artifact.
Only a few of the people the Emperor changed survived. The Emperor retreated inside the prism and began helping and directing the characters toward the eventual confrontation with the Absolute.
Snatching people up in plain view like the Emperor was doing was not how the chosen of the dead three were pursuing their goals. It was the result of the Emperor trying to build a force to fight back to ultimately free himself.
The suggestion that process was interrupted by not getting to Moonrise was supposition. That was never the case. The process is not something that's finished at Moonrise. When that possibility is mentioned to Halsin in the worg pens, even he expresses some skepticism, saying essentially that he wouldn't rely on blind luck, or something to that effect.