Because the companions + the PC was on the ship? It doesn't make any sense if this was a completely random nautiloid operated by uninvolved mindflayers, because then the whole story thread about searching for information on the cult of the Absolute is a thing.
Of course, sorry for the confusion, I thought you might have meant more with it than the obvious (English is not my first language).
I still think
the Emperor coming close to SH, breaking free from the brain's influence thanks to the artifact and then tadpoling SH is the best explanation. The Intro showed people being teleported directly into the pods by the tentacles so maybe no other mindflayer than the Emperor came close enough to SH to be affected by it. (I won't die on this hill though)
