Just a nit -- Us aren't a tadpole creation/mindflayer, we're an Intellect Devourer: we're a whole different thing unrelated to the Illithid tadpole process.
Edit: On second thought, I guess you were referring to Us recognising the tadpole in us, in which case scratch the above nitpick, it's irrelevant.
But I do think (though I don't remember the encounter very well, I always click through it hastily nowadays) it's not the tadpole we react to, we just assume we are enthralled like the other mind-slaves you encounter on the ship.
There is the thing I wonder with Us, do they assume we are enthralled? They seem happy enough to fight the thralls and intellect devourers as well as the mindflayer, so I wonder if they had somehow imprinted on the player or got connected to our Tadpole in particular, and if Mutilation and/or the fact we had to remove Us from the cranium has some role to play?