Kot-- Kot.
It takes 13 years, for them to become psykers.
Before then, they are not. In that time, there is insufficient chaos in the area to do that kind of trick; The systems inside would not be at risk, because there is no source of chaos to do it. The autotermination system would activate before that transformation happens, so there is never a point where the system that does the indoctrination would be at high risk.
You keep returning to the "BUT PSYKERS!!! OMG!"--- while ignoring that it is a sudden, and profound change for them.
Also, Parallel time.
I will pick on christianity.
Christianity teaches that the time you are alive, is not the real reality; The real reality is a spiritual reality with God presiding over everything. As such, the sufferings of the body are meaningless. The wants, needs, urges of the flesh are to be abstained from, and focus given to the spiritual.
This is a real reality; People hold to this set of doctrines, even when there is no evidence.
This would be similar. The child would be told, straight up, that what they are experiencing is not real. That the real reality will be made manifest to them when they are older, and that they need to be prepared for it, or it will destroy them. This is the truth. They would grow up with this knowledge, and it would be true belief for them. They would grow up with the experiences of the simulated reality, but they would already beleive those experiences to be false. In that time, they would have had simulated encounters with the immaterium as part of their training, to better prepare them for the real reality they would experience.
Again, a powerful mind can reshape the immaterium. See also, the big assed beacon Big E projects into it.
While the immaterium is dominated by hell, the idea is to put enough of these beings into action, that their combined mental energy transforms the immaterium. The immaterium was not always a hell. It is not necessary for it to be one.