Elemental Penetration should apply to Damage Over Time as well. With so many different forms of elemental penetration available, the fact this isn't used in DoT calculations is very bizarre. A simple change like this can go a long way toward alleviating the major issues presented with the Elemental Damage Over Time issues other posters have brought up in the wake of EE/EO's changes.
This is not a "simple change". This fundamentally cannot happen without completely rewriting everything to do with taking damage over time from the ground up to be massively less efficient.