Not all flights to USA from Vancouver and other Canadian cities travel to airports with customs services available hence the clearing in the departure city. I know that it's been happening for 40 years.
I do believe that flights to Canada from other countries have to arrive a airports specified by the Canadian authorities thus I understand there is no Canadian customs clearance done in US cities/towns - at least this was the case in my days living in USA and travelling to Canada at least once a month for a few years.