In Noel Canning, strong evidence was presented that recess appointments were understood originally to mean the recess between sessions of the Senate. From this point, it follows that Congress could (and probably had to) give the President the power to make interim appointments during a session when the Senate was on a break. Thus, there was no conflict between the two so long as the interim appointment was time limited or there was some clear norm that a formal nomination would quickly follow for Senate consideration.
Given the modern interpretation of the Recess Appointment Clause (in other words, that these picks can happen whenever the Senate says that it is in recess), and the fact that a President might want to avoid Senate confirmation for one of these positions, I think that there is a conflict or a problem. In practice, though, if Whitaker does nothing of consequence until a nominee is chosen, then I doubt a court will gainsay the OLC Memo’s conclusion.