Wind Damage
We have many 50mph + storms a year. 3-tab roofs are not meant to handle that high of a wind rating. 2 layer 3-tab roofs have a higher probability of being damaged.
Since the 2nd layer can't breath, the shingle just bakes on the roof causing it to become brittle. The wind hits the rake end and flips the shingle over.
Wind finds the weak shingles and will either flip them up and crease them, or rip the shingle out completely.