Are Canadian flights included in the Domestic US DOT Form 41 dataset?

Yes, flights between the USA and Canada are included in the "Domestic" Form 41 dataset. 

The US Department of Transportation Aviation Policy states:

Certain data in this review are classified in two broad categories: namely “Domestic” and “International” services. “Domestic” service encompasses operations within and between the 50 states of the United States, the District of Columbia, the Commonwealth of Puerto Rico, and the U.S. Virgin Islands. It also encompasses Canadian transborder operations and Mexican transborder operations.

https://www.transportation.gov/policy/aviation-policy/airline-quarterly-financial-review