"Think Assassins Creed."
What makes you think I've played Assassin's Creed?
"To get connected to a memory you need a full synchronization. But introducing new foreign information results in disrupting the once stable harmony. As a result, you make the victim assume that the general understood reality within the matrix of people to be real."
That makes sense.
I don't really get the other stuff you're saying though. I don't think Pilot's insanity makes him an anti-Cancer entity. Aside from the initial restart, it didn't seem to be affected by it. And I don't think Snippy's hallucinations have anything to do with Pilot's insanity.
"You never see Snippy wake up and shake his head over a bad nightmare"
Yeah, you do. You see it the first time Cancer integrates him.
"you see a frustrated Snippy trying to strangle Pilot."
That's because at the time he'd been strangling Pilot in his memory/dream/thing.