Certainly possible, but my impression is that we saw what would have happened to us in the pod you can activate. We can be turned to full-blown mind flayers with a push of a lever. I doubt they let just any random people they pick up lead the troops of the absolute, much more likely those are picked and chosen from already loyal followers instead of the randomness of a nautiloid abduction.
I suspect that they had a fairly strong selection of candidates. Some have certainly been used to create intellect devourer and some have been used as mind flayers. Probably only some of the captured were to be true souls.
