I don't think a mindflayer is on par with an elder brain, or a netherbrain, in scheming capacity. That seems deeply counter intuitive. Illithid are extremely arrogant, even if you're allied, it would despise you too much for being a less evolved lifeform, yet top dog.
It isn't, but an elder brain whose mind is dominated by a top-notch Netherese artifact is also not on par in scheming capacity against its own master as a free elder brain would be. An Illithid with all three netherstones combined into one like the infinity gauntlet may very well be what it takes to completely subdue it until such point at which an outside force manages to steal your netherstones or employ greater divine/magical/psionic energy than even the Crown itself can field.
According to the Netherbrain, the three's scheme of fragmented command has never *really* worked, the brain just pretended it did to bide its time. The game does relay however that Illtihi-Tav, holding the combined stones, has well and truly subjugated the brain, and the mental fortitude of retaining that status could be viable for an Illithid.
The biggest danger is once again, in my opinion, an outside force interfering with the bond as opposed to Netherbrain rebellion.
