It could be that they did not have enough time to include all the content for the absolute side. Some things are broken.
The absolute wants the crash survivors dead. The player was not supposed to be a true soul.
The mindflayer revealed:
"curved drow blades, crude goblin torches, gnoll teeth dripping blood
You see other mindflayers arranged in a seren circle. Absolute unity. Absolute power"
I am not sure whether or not the vision for the githyanki chase was a memory of the distant past or something that could happen. The Gith once fought the mindflayers and they had lots of nautiloids back then. But if the Gith hunted the nautiloid because they know that something like it is about to happen again then the mindflayers posess a fleet of ships once more.
