I think that's possible and can certainly be your head canon or what you run at your table.
That said, I believe the connections between the two are entirely due to the githyanki's enslavement by the illithids. Learning the wrong lessons from their oppressors is a sad, but not unbelievable, outcome. The note about aboleths is interesting but I'm not familiar enough with their lore to effectively speculate why they would not know about illithids - perhaps they just didn't come into contact with them until the height of the illithid empire.
This kind of lore stuff is why I stick to homebrew tbh