Yeah, Shapiro likely sets up the guidelines, Atkins has to make moves based on those guidelines, and Shapiro signs off on everything in the end. I don't think Shapiro has the low OBP/exit velocity/35% K% fetish, although I didn't pay close attention to his run in Cleveland, so who knows. Seems like Atkins and his crew handle the actual moves.
I'm really curious to see how the Shapiro/Rogers thing plays out. If they really wanted him long term, a deal would have been agreed to already, or at least before the off season begins. Every time Shapiro is asked about it, he tap dances around it. Clearly if they let him walk, or he decides to leave, he would get a job pretty easily, so there's no real desperation on his part I'm sure. Ed Rogers hired Shapiro, so maybe we should trust his judgment, but he did try to tamper to get Kenny Williams and Dan Duquette before that, so it's kind of frightening to think about what the next Jays front office might look like if Shapiro leaves.