Yes and no. There are complications with it.
Let's take my own field as a lawyer. Lawyers are provincially regulated. There is no federal bar that would approve my standing as a lawyer. The federal government hires lawyers, and they require the lawyers to be recognized and registered as lawyers in one of the provincial jurisdictions. If it were to decide it would have its own standards and certify an individual as being a lawyer for its purposes, but that individual had no recognition by any of the regulatory officials, that lawyer might not be terribly useful to them.
So it's a bit of an artificial question, because the individual has to work in a larger economic field than just the federal field. While it may theoretically be possible in some fields for the federal government to decide that this individual is going to work for us and only for us, so we'll decide whether he's qualified to fly a plane or not and don't need provincial authorities to tell us, there may nonetheless be other reasons why some recognition outside of the federal level should be obtained.
Going to that particular example of pilots—and I don't know for sure whether I'm right in saying this, so I again qualify what I'm saying, but I'm curious now and will double-check to see whether this is the case—it seems to me that if the airlines are federally regulated and provinces have no jurisdiction in regulating airlines, then yes, the federal government would have the ability to decide whether someone is qualified to fly a plane. So with some caveat, that makes sense to me, but I'd want to double-check to see whether the feds are actually doing this or have chosen to accept provincial control of that area too.