They ignore Mod2s DoT Shielding / Spell Shielding, the spells Bombing Bugs and Explosive Seeds as seen in the Endless War HA, both hit for the same value whether you have 35% or 0% (ie naked) of their respective mod2 Shielding. It is most likely that spells using this same calculation/data/whatever in regards to scaling also are ignoring mod2s.
