The ability to take non-continuous trips on a single fare on Presto has been well reported in the Presto thread.
I'd expect there is a "huge matrix" listing all the TTC routes and the transfer opportunities for each route. However, because TTC customers aren't always required to tap on/off when entering/leaving a fare-paid zone, it is frequently impossible to determine conclusively whether or not certain trips are continuous. In cases where it can't be determined, the system likely defaults to a two hour transfer rule.
For example, if you tap on anywhere on the 29 Dufferin, and then tap on the Islington bus 30 mins later, I'd expect that you'd be charged another fare, as there's no way to travel between those two routes without being forced to tap on (all subway and surface routes connecting to 29 Dufferin require a tap)
However, if you were to tap on at St Andrew Station, and then tap again on the 511 Bathurst streetcar at the Bathurst @ Fleet St stop within two hours, you wouldn't ever be charged another fare, because it is possible to make a continuous between those two points without tapping.
In a more extreme example, you could tap on the Bathurst Streetcar and tap again on the Lawrence East bus at the Kennedy @ Lawrence stop, and not be charged, because it's possible to make a continuous trip there without tapping
Because the TTC network affords so many opportunities to transfer vehicles without tapping, I would not be surprised to learn that most Presto trips on the network are defaulting to the two hours rule.