Hear is your answer:
Magura recommends when the pad is 2.5mm, that is the actual brake pad and the metal backing plate. Yes Magura gives you that yellow disc tab that has a slot cut out. Basically if the pad fits in the slot, time to replace. No sense in gouging your rotors with the metal backing plate and having to replace $60 wavy rotors.
I'm pretty positive avid recommends changing the pads when the actual pad and backing plate is 3mm thick.