The effect would be that, if a first nations law was enacted, for example, by a coastal first nation that somehow affected shipping, and that first nations law conflicted with the federal navigable waters protection act, for example, you could have a situation where it's not clear whose act is to prevail. The first nation might say its act should prevail because it's in its jurisdiction in its coastal waters.
The idea of the federal paramountcy here is to ensure that there's a rule to address a conflict in that sort of situation.