So I do have confirmation critical roll modifiers stack/cancel from another rules question so that part I am glad is confirmed because I was largely assuming.
I am inclined to think Penetrating Critical checks are based off final damage rather than modified because otherwise that could lead to some weirdness with weapons/specialty ammos that would otherwise not be able to do damage, or reduced damage without Direct/Glancing Blows being used, still being able to cause Penetrating Critical checks.