You're right, it is an unusual thing to see in legislation. Normally when an act is to be preferred over another act, it states in that act that, “Notwithstanding any other act....”
It's highly unusual to see an act that's made subordinate to everything, because there's no way of predicting in the future what other legislation may be made that perhaps Parliament doesn't really want the Aeronautics Act to be subordinate to, but an amendment like this would have the result of making the Aeronautics Act subordinate to anything until you had an opportunity to come back to the Aeronautics Act to amend the clause.
From the Department of Justice's point of view, it's not sufficiently concrete. It would lead to vagueness and uncertainty in the future. It would be confusing to interpret the statutes and to know with certainty whether that's really the intent. If other statutes were passed, each one would have to take into consideration the status of the Aeronautics Act in order to make it clear whether Parliament really wanted the Aeronautics Act to be subordinate to that piece of legislation. You would have to take that into consideration with each new piece of legislation, and perhaps with what's on the books now, go through everything to determine if that is indeed your intent.