That's not a post hoc rationalization. The illithid will always be a threat until Wizards publishes a book that says they're not.
Literally anything in the monster manual is a threat so I have no idea what you're getting at.
It's organic storytelling not "planned all along." Of course it wasn't planned, and they're not saying it was either, that's your head canon.
So if your whole point so far was not "making the illithids from the BG2 side quest the main villains is not lame because there was foreshadowing", then what was?
Also, how is my head canon the very thing I'm arguing against???????