If you're in Business Class, you'll be among the first off the train and if you hustle and have no checked bags, you'd be the first through Customs. That said, I agree that the timing is not in your favor in this case.

FWIW, if you trip was later in the day, I'd suggest the Amtrak Thruway bus, because there's a stop in Richmond, BC on the way in to Vancouver proper. The hotel that the Thruway bus stops at has a free shuttle to the airport, though I'm not sure if it's available to Amtrak bus passengers. (It would be a relatively quick and cheap cab ride, in any case, and would be much quicker than going all the way in to downtown Vancouver first)

It's also an option if you have a first-thing-in-the-morning flight from YVR...you catch an evening bus, get a good night's sleep, then get the free shuttle to the airport in the morning.

However, for a mid-day flight, the Amtrak-to-Richmond route doesn't really work.