I can't comment on the duplicate booking strictness, but T1 to T3 will only take 5-10 mins. There is a frequent train outside of security.

The main disadvantage I see is that you'll have to clear CDN customs in T1, whereas if you were not changing terminals and had a boarding pass for your WAS flight you could go directly to US customs in T1. Do you have NEXUS or only GE? If no NEXUS, I'd budget an additional 30 mins to clear customs.