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It's a rare thing to see the direct route costing significantly less than the connection.
No it's not rare, that's how Via's fare system works. If your trip involves two legs, they just sum the ticket prices as if they were two completely separate journeys. So you pay the base price twice.
See for example a trip from Aldershot to Oshawa on a random Wednesday a month from now. It gives you options like this one on trains 76 and 46 with a 44 minute transfer in Toronto, which costs $40.
Which is the sum of the individual tickets on trains 76 and 48:
Surprisingly, even with a 44-minute transfer, the Via trip is significantly faster than the direct GO train, so some people might actually use Via for this station pair if the prices were less insane and Via service was at all reliable.
The two service alerts were that one of the elevators in Union station is out of service
For the same price as the 107 km trip from Aldershot to Oshawa, you could travel on train 48 for 290 km from Toronto to Gananoque:
Or travel on train 76 for 185 km from London to Toronto:
Sometimes the trip planner doesn't even let you transfer at all.
Port Hope, Trenton, Napanee and Gananoque are only served by Toronto-Ottawa trains while Cornwall is only served by Toronto-Montréal trains. So to get from one of those stations to Cornwall you would need to transfer in Kingston or Brockville. For example:
VIA 54 Toronto-Ottawa (daily)
18:39 Port Hope
19:15 Trenton Junction
19:50 Napanee
20:09 Kingston
VIA 668 Toronto-Montréal (weekdays)
20:25 Kingston
21:51 Cornwall
But if you try to actually book a train from any of those stations to Cornwall the website tells you it's impossible. Even if you consider a 16-minute transfer to be too short (despite both trains being on the same track and therefore affected by the same delays), there's another possible connection from train 42 to 66 with a 3h transfer in Kingston.