I've dug further and AS provides a tool to confirm what documents are required (
https://alaskaairlines.traveldoc.aero). Here is what it says...
Passengers holding a NEXUS card may only use this document in lieu of a national passport if the passenger is travelling directly from the United States to one of the following NEXUS designated airports in Canada:
Calgary International Airport (YYC),
Edmonton International Airport (YEG),
Halifax Robert L. Stanfield International Airport (YHZ),
Montréal-Pierre Elliott Trudeau International Airport (YUL),
Ottawa Macdonald-Cartier International Airport (YOW),
Toronto Billy Bishop City Airport (YTZ),
Toronto Pearson International Airport (YYZ),
Vancouver International Airport (YVR) or
Winnipeg James Armstrong Richardson International Airport (YWG).
Passengers holding a NEXUS card may use this document in lieu of a national passport, provided the passenger is travelling directly from one of the following NEXUS designated airports in Canada to the United States:
Calgary International Airport (YYC),
Edmonton International Airport (YEG),
Halifax Robert L. Stanfield International Airport (YHZ),
Montréal-Pierre Elliott Trudeau International Airport (YUL),
Ottawa Macdonald-Cartier International Airport (YOW),
Toronto Pearson International Airport (YYZ),
Vancouver International Airport (YVR), or
Winnipeg James Armstrong Richardson International Airport (YWG).
Given that this information comes directly from AS website it seems reasonable that agents working these routes know both the applicable government and company rules.