It really only comes into question when the two statutes are in conflict. The scope and the authorities of the Aeronautics Act, fortunately, are put into a fairly confined space; it's pretty identifiable.
You do get the possibility of conflict when other statutes affect people affected by the Aeronautics Act. Examples are the Canada Labour Code and the Canadian Transportation Accident Investigation and Safety Board Act. I think the Transportation of Dangerous Goods Act is the other one you're concerned about. But you only need the overriding clause when there's going to be a real conflict. It's been my experience with the Aeronautics Act that generally either there is a shared jurisdiction and the two things are compatible, or it's not really a conflict; the two things operate in separate spheres and don't intrude on one another.