It is quite clear he needed to catch all 3 bodies and we didn't see the remaining 3 in this genjutsu.
Nagato shares his consciousness with the corpses but it's not like he's suddenly getting put into a genjutsu if one of his bodies gets caught into a genjutsu. Wasn't even one Pain put in a genjutsu in Konohagakure specifically so that this Pain could be interrogated?
Because the others weren't actually revealed yet, it was that mystery which led to Jiraiya's defeat when they surprised him, you're asking for Kishimoto to randomly focus on the other paths who didn't exist in the readers mind yet and spoil it which makes no sense.
That's literally what would happen if you think about this logically, Genjutsu controls a person's senses and psyche, the corpses do not have this, the only senses or psyche that can be controlled are Nagato's.
And we see that Nagato remembers Jiraiya's words that he said to Nagato's puppets while they were under the Genjutsu
One of the Pain's being interrogated by Ibiki is just anime filler I'm pretty sure.