Using presto...
I took the Queen Streetcar Eastbound to Queen Station, tapped in at the faregate to "transfer" and went Northbound to Dundas Station. [1 trip with 1 transfer]
About an hour later, I took the Queen Streetcar back home Westbound from University Ave. [1 trip with 0 transfers]
I was only charged once, and my trip back home was counted as another transfer payment.
After reading other posts, it seems that the Presto readers are unable to detect what is a complete trip on the TTC, at least with the current set-up. Although the same transfer "rules" apply with Presto, I doubt fare inspectors / the ttc would be able to justify giving you a fine if you tapped your presto card in good faith, thinking it was a new trip when it turned out to be a "transfer" payment, as this is technically fare evasion. There is also no way to tell on the readers if your trip was counted as a fare deduction or transfer payment, although other agencies such as OC Transpo use the exact same readers but it tells you after you tap how much money you have left, transfer time remaining etc.
I can see this becoming an issue for the TTC in the months to come if they do not resolve this. If there is truly no way for Presto in its current form to detect what constitutes as a complete trip, the TTC might be forced to indirectly adopt a time based transfer system sooner than they thought.