Personally speaking, I know of no situation whereby a foreign-owned boat in the pure legal, commercial, business sense of ownership can actually fish in Canadian waters and transfer out the fish. All I know is that in places like the north, generally speaking, or in all cases, the majority ownership--albeit maybe a small percentage, if that's what it is--is a Canadian-flagged vessel. If it's a Canadian-flagged vessel, regardless of who's behind it with dollars and commercial interest, it has a Canadian flag and hence is then managed as a Canadian unit by DFO.
That's to the best of my knowledge.