It's not quite the same, but on my way up to Montreal from Burlington most recently, I got off of I-89 before Highgate Springs and cut across the north end of Lake Champlain, entering Canada at the Rouses Point crossing. There was only one car ahead of me and the questioning was considerably less intense than at other, larger checkpoints. I was half expecting to be asked why going out of my way to use a secondary checkpoint, but I received no such inquiry. I was through in at most a couple of minutes. And that was also with an Amtrak train clearing customs at the same time, which I'm sure kept much of the customs staff occupied.

I recommend you check the CBSA website as you approach Champlain to check on the border wait times (updated hourly). If it's more than ten minutes, it's probably worth getting off the highway and dealing with the side roads.