I've found AC agents to be enormously flexible on this matter for connecting flights, even on the worst fares imagineable, or even Aeroplan reward tickets for that matter. (ie: they'll even turn a convoluted multi-segment reward itinerary into a nonstop if there's seats available.)

Where they aren't flexible is when you show up at the airport for your first flight of an itinerary, and want to get on early. Almost always, then, you will be hit with standby and/or change fees.