There's no indication though there will be the same fare from Weston to Pearson (or say Weston to Bloor) as Union to Pearson. Nor is the auditor saying that will be the fare. That's what the auditor thinks the fare would be to break even. Whether Metrolinx and the government chooses to do this or not remains unclear.
It's also unclear what there fare will be for those who travel on the line every day, compared to those using Presto, compared to those who are buying cash tickets. Take Vancouver Airport. The regular Skytrain fare from stations near the airport to downtown is $4 cash or $3.15 with a book of 10 tickets amd $124 for a monthly pass. However a person landing on a plane and buying a ticket at the Airport station pays $9 - but someone who has a book of 10 ticket only pays $3.15. Obviously Toronto pricing will be very different ... but the concept might hold.