SN 12.51 Why are meritorious formations rooted in ignorance?
It seems to me that meritorious formations would be rooted in ignorance because wisdom would see the emptiness of such formations. If ignorance is abandoned then such formations and their karmic functions cease to play a role. They have been transcended.     

Perhaps one could see this as progressing from the teachings of the first 'Turning' to the fundamental teachings of the third.    

EDIT: In the third Turning of the Wheel of Dharma the Buddha "taught about the Buddha nature, the enlightened essence of luminous clarity that is the true nature of the mind of every sentient being." 

This is the stage of thorough analysis in which, "in order to help his disciples abandon their clinging to non-existence, the Buddha taught that genuine reality transcends the conceptual fabrications of existence and non-existence, appearance and emptiness, and any other notion of what it might be."        

Quotes are from The Sun of Wisdom by Khenpo Tsultrim Gyamptso