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Assuming Magnus is at full wounds and gets a +2 to his casting roll, how does this affect his ability to Peril (if at all)? Does he still Peril on natural 1s and 6s without regard to his casting bonus, or does he only Peril when he rolls a natural 10 (because it gets bumped up to 12) and he can't Peril from double 1s (because that automatically gets bumped up to 4)?

The rule for Perils states double 1's and double 6's. Not a 2 or a 12. So yes, Magnus Perils the same as any other Psyker.