Hi Ryce;
I only recently became aware about the distinction between when you can and when you cannot boost your penetration with AC, etc., and it led to parts of the discussion in this thread.
Personally my preference is clear: always to allow boosted penetration. My remaining challenge is to figure how I'll go about it in practice, what with having possible different penetration of the same spell versus different MRs. I'm considering suggesting a HR to my troupe that if a spell has boosted penetration then that spell's effect has penetration of '0' toward all other MRs.