Nice idea, but you're asking bureaucrats to think outside their silos. This would require the City to set up a separate process to identify and charge riders, or to work in cooperation with the Province to charge through plate registration. Staff are just looking for the easiest way to maximize revenues without extra work or concerns about fairness (proportional charging across the City).
If the City & Province could actually work together, we'd have a zone system for transit fares where you could ride any vehicle run by any operator within the City for the price of a Metropass. Just think about it. Connecting Main GO & TTC stations could allow the GO Lakeshore line act as the eastern relief line to Union. Both the GO Brampton Line and the Union Pearson Express could act as the western relief line from Dundas W TTC station, and the Richmond Hill line could relieve the Yonge subway with 1 stop from Leslie station on the Sheppard line to Union. So instead of saving billions in capital expenses that duplicate services, they implement additional charges ($60/month to ride 1 stop from Liberty Village to Union) in a meager attempt to imply cooperation, which no one (ok, 134 people) are prepared to pay extra to use.
Sorry, rant over! It's just that logical thinking only works in this City if it falls in line with political agendas.