As noted above, IRROPS situations are different (also tax treatment for flights that are only between US and Canada is different and fares between the US and Canada are symmetric).

While they can waive any fare difference for schedule changes, just because they are charging the same base fare on the non-stop vs. US connecting flight does not mean the tax treatment is the same and they will necessarily eat the additional taxes (US Customs/Immigration/APHIS/TSA/PFCs) that are involved with connecting via the US vs. flying non-stop. Most of these additional taxes are due to the US not having the concept of international transit and requiring that you actually enter US when just transiting (and pay the taxes for doing so).