Interesting idea.........
@Urban Sky could comment on if there would be any issue w/Amtrak crews operating the train for that brief distance inside Canada from VIA's perspective.
Beyond that, I do see a few challenges. Given that Empire / Maple Leaf Service has a real challenge staying on time, even before factoring in customs, you would have to have a GO Train expressly dedicated to meeting that Amtrak train, which poses schedule/clearance issues.
There is the matter that VIA would not longer be in a position to sell tickets to NYC and GO and Amtrak would have to code-share to allow the NYC/Rochester/Buffalo ticket to be bought through one or the other.
While Empire service isn't luxurious by any means, I would consider GO rolling stock/service a downgrade, that might impact traffic levels.
You're also now potentially adding customs clearance delays for the Empire service which currently doesn't have that issue.