He wants you to "evolve" into a mind flayer throughout the game after all... and I have no doubt that he's after the Grand Design with himself in control. He's an Illithid after all.
That's like saying you absolutely can't trust a word from orpheus either because the githyanki want their own 'grand design' to conquer and enslave everyone. But at the end neither the emperor or orpheus tries to dominate the brain for themselves
