Embraer and Boeing will base their JV on a newly created company, of which Boeing will own 51%. That company will only handle the commercial side of Embraer; the military and corporate sides will remain solely under Brazilian control.
It would come as a great surprise if there wasn't some kind of scope clause on the JV, along the lines of 'research, develop, manufacture and market commercial aircraft with a seating capacity between X and Y'
So, no, Boeing won't be selling Super Tucanos or Phenoms.