Might have had something to do with why it and the quests related to it were mostly cut (although time constraints were said to have been the problem). Seemed like there was meant to be some greater conspiracy involving the various evil groups in the game, including all the different slaver movements (they're freaking everywhere!), the Twisted Rune (who were allied with the Shadow Thieves to some extent...who had slavery connections themselves), the skinners (who make some kind of reference to the Twisted Rune, IIRC), the de'Arnise Keep invasion (who Tor'Gal mentions as having been directed by someone else, someone stronger that he feared - not someone who simply paid him off like the Roenalls might've...although now that I think of it, the Roenalls were involved with the slavers, too! Further, Tor'Gal was working with Umber Hulks, who are...unusual monsters that seemed to always be in mindflayers' company...and also Glacias, who was apparently permanently dominated and helped betray de'Arnise, who was ardently anti-slaver, IIRC), and possibly the mindflayer infestation in the sewers (along with the Hidden and the Jysstev nobles...and there's a note that mentions them soon taking control of the entire..., but doesn't specify what)...who were also possibly connected to Firkraag but at the very least Tazok. Whatever it was supposed to be never fully apparated, though.
(e): I'm reading elsewhere that it even goes back to Durlag's Tower, where it was said that the doppelgangers were directed by the mindflayers as well. And with that connection, suddenly you have to wonder about the Iron Throne and Sarevok who also had doppelgangers in their employ...and Tazok, who held the key to the mindflayers' secret layer. FURTHER furthermore, if Sarevok was involved with the mindflayers, suddenly we have a connection back to Firkraag again - Firkraag was seeking revenge against Gorion for unspecified actions during his Harper days, and what do you know, the first thing that happens in BG1 is that Sarevok tears Gorion to shreds. Egads, the connections are everywhere! There are even connections to Irenicus and the Githyanki (Irenicus had part of the Silver Sword...and also, the Githyanki were in the Drow City at the time you and Irenicus go into the Underdark, while the Matron Mother's daughter is also kidnapped by the mindflayers? So many connections...): https://forums.beamdog.com/discussion/4030/the-great-shadows-of-amn-conspiracy/p1
Out of curiosity, I started reading about the origin of the mindflayers in the D&D cosmology. It seems like there's no concrete explanation for their origin. One explanation is that they're from the "Far Realm", an incomprehensible alien realm that's considered to be outside the normal cosmological boundaries that's home to hyperintelligent cosmological alien horrors. Another explanation is that they're a group of space and time travelers that were facing annihilation at the end of time, and so traveled back to try to make their home in the past. Whichever way you look at it, it seems as though they're essentially an alien race...and they're...secretly trying to seize control? So it's basically an X-Files-esque alien invasion, I guess. Huh. Goes well with the slavery elements.
iirc phaerimm are literally flying polyps. Illithids are supposed to be Yithians.