I always hated that line: "Since you're still here, we assume you've won."
Well, thanks for all your
fabulous help, sister ship!
Here are my theories:
All of the domed ships had good communications with each other immediately departing Palma. This would make sense considering that if one of the ships found a habitable planet, you'd want the others to know about it. That is, if they weren't traveling together already. Or, well, you'd want to have contact, anyway. Safety in numbers and all that.
Palma knew something was going wrong with Algol and had enough time to build a fleet of these incredible ships, so I'm guessing there was
some knowledge that DF was behind things. When Alis left Copto to return to Algol, her departing words included something about a bigger threat awakening in Algol. That was a few hundred years before PSII. That might have been about the time Palma started building their fleet. Perhaps this is also the start of understanding DF's cycles.
Perhaps the ships never intended to cease communicating with each other, but
Alisa III's communications were compromised during the Devastation War. Perhaps the communications were restored once DF was defeated by the third-generation hero, and Neo Palm, though it "felt" the DF's presence, couldn't really help that much (other than to be on standby), since communications were nonexistent, thus making access between ships impossible to coordinate.
Perhaps
Alisa III and
Neo Palm were chosen by DF to be the last of the fleet to destroy because they included more important leaders and Espers, thus being harder for DF to annihilate. If I'm going with this theory, then it stands to reason that
Neo Palm is actually
the most important ship of all the Palman ships, since DF was trapped on
Alisa III before he could destroy it and move on to the final ship. Perhaps it houses Camineet, or whatever the seat of government was at the time.
My own theory, then, is that DF simply hadn't made his way to
Neo Palm yet, that he was stuck on
Alisa III, and that
Neo Palm knew about DF because there were enough Espers, prophets, etc. that knew it was his time and were aware that they could no longer communicate with
Alisa III because DF was on that ship, and finally, because
Neo Palm knew there were no other domed ships left in the fleet.
Neo Palm either knew in Sean's story that getting too close to
Alisa III was risky due to the DF compromise, or was fortunately late to the scene (it sounds in the script like it was a bit of both: It knew about DF and was coming to help, but was fashionably late in arrival).
Whew.