An official quote will probably be appropriate:
"Mark then sins that laid our mighty forbears low and learn well their lessons:
Make not a machine that suffers to think as a man,
Worship not the false god of progress,
And stare not too long into the darkness within,
For the first lies horror, the second ruin and the third eternal regret..."
Well, for one, any SANCTIONED Mechanicus cogitator core is quite incapable of Abominable Intelligence. Hypothetically, if a Magos was to fully replace all their brain-matter they suddenly wouldn't cast a shadow in the warp due to a fully mechanized sentience (similar to a Necron). If they knew that much they'd have to take precautions around psykers to not give away tell-tale signs but it would still be a matter of time before one of his contemporaries noticed something "off" and look further into it (if not the Inquisition proper).
Though Machine is pure and the biological inferior one can never fully cast it off for that would mark one as a Abominable Intelligence but, in augmenting the left cortex through excising and replacing the right, the mind can be made to commune with the machine as an equal in capacity. Both of these contradictory elements have to be followed or the Folly of the Iron Men will be repeated.