Okay, here is the official way that various penetration effects work:
First, apply any Reduction effects, like Taric's Shatter Active, Soraka's Starcall, Black Cleaver's Stack, Fiddlesticks' Aura, etc. This CAN go negative.
Second, apply any percentage-based Penetration effects (Last Whisper, Archaic Knowledge, Void Staff). This clearly cannot go negative, because the highest you can get is 55%.
Lastly, apply any flat Penetration Effects (Sunder Mastery, Runes, Brutalizer, Sorc Boots, Haunting Visage, etc). This cannot go below 0.