The drafters could do that. It's clause 49 of the bill, the coming into force, the very last provision in the bill. It says:
The provisions of this Act come into force on a day or days to be fixed by order of the Governor in Council.
So other provisions of the bill could be brought into force immediately upon royal assent, or shortly thereafter, and the provisions dealing with designation could be brought in at a later date. There is no problem with doing that.