Magic Craftsmanship works exactly like Craftsmanship, it depends on the recipe as to which is used. Qualtiy gain is dependent on your attributes and the tool used.
I am surprised you got to rank 40 without ever noticing this...Hell, SE themselves explained this much. >_>
And Obei, both hands can yield high quality for finished items and Toxic Powder uses Craftsmanship...so logically you would use the main hand unless doing it for items.