I've never been asked to pay a change fee when arriving early, or hustling from a connecting flight at YVR to the downstairs desk near the regional gates and getting on an earlier than scheduled YYJ flight. Sure sometimes I'm there too late, or the flight is full, but never had them ask for a change fee just to get a spot on an earlier flight. I typically don't travel with checked luggage which could pose additional problems if you do.
In your case I might have gone through security and talked to the desk down near the regional gates rather than ask the check-in agent, worst case scenario they say no, you go back landslide and take the ferry as you mentioned. At 4:30 I know the check in line can be ridiculous and so they may not have been able / willing to take the time to make the change?