There is a province or two that allow more than three when loaded with slugs, possibly buckshot as well, but not sure about that. BC is one, maybe Alberta as well. The Migratory Game Bird Treaty is a Federal treaty, as you say, but the administration of at least that part of it dealing with shotgun capacities when hunting migratory game birds is left to the provinces. Ontario and others have decided that it's just easier and leaves less wiggle room for poachers to squeeze through to limit all shotguns, for all hunting to three rounds combined
You may very well be right. I had checked with a few jurisdictions a while back, and they all had 3 shells in the shotgun while hunting specified. I have a Savage 20 gauge bolt gun with rifled barrel, and the detachable mag only holds 2 shells. I have not seen any larger mags offered for it (although I haven't really looked), so I imagine the 3 shot rule must apply pretty well all over, otherwise, you'd think they would supply larger mags and a plug.