SN 12.51 Why are meritorious formations rooted in ignorance? SN 12.51 says:


  Bhikkhus, if a person immersed in ignorance generates a meritorious volitional formation, consciousness fares on to the meritorious; if he
  generates a demeritorious volitional formation, consciousness fares on
  to the demeritorious; if he generates an imperturbable volitional
  formation, consciousness fares on to the imperturbable. But when a
  bhikkhu has abandoned ignorance and aroused true knowledge, then, with
  the fading away of ignorance and the arising of true knowledge, he
  does not generate a meritorious volitional formation, or a
  demeritorious volitional formation, or an imperturbable volitional
  formation. Since he does not generate or fashion volitional
  formations, he does not cling to anything in the world. Not clinging,
  he is not agitated. Not being agitated, he personally attains Nibbāna.
  He understands: ‘Destroyed is birth, the holy life has been lived,
  what had to be done has been done, there is no more for this state of
  being.’


Why are meritorious formations rooted in ignorance? 

Also, since MN 117 says the Noble Eighfold Path and its Two Noble Fruits are "kusala", are meritorious formations "wholesome" or "skilful" ("kusala"? Or is there a difference between the words "meritorious" ("puññā") and "skilful" ("kusala")?


  So there are twenty on the side of the skillful, and twenty on the side of the unskillful.
  
  Iti kho, bhikkhave, vīsati kusalapakkhā, vīsati akusalapakkhā—
  
  MN 117
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