The ocean is a part of coastal provinces in a way that is not always clear to those who think of territory as land and water as a transportation route. For coastal states, the ocean is an inseparable part of the life of the state, which is why international law gives states ownership of their ocean in the first place. If Alberta separated, they'd take their land with them. If BC separated, they'd take their land and their ocean. It is BC's ocean in a real sense, and constitutionally Canada's.

In recognition of that, the Canadian government doesn't in fact rule over Canada's oceans and ports with an iron fist. And let's not pretend any province has objected to a railway being built across it, or that any hydro lines or pipelines have been built without at least grudging consent of the provinces or territories they traverse through. The problem here is a political failure to build an agreement. It's simplistic to think an assertion of federal authority can fix that failure.