I'll admit that I haven't read the whole assessment that was just released (too big!), but it comes from a long-running program that has funded many port-related emission studies and programs around the country including in the LA area. The assessment could (but doesn't necessarily have to, and certainly won't applied be the same everywhere) lead to new or revised regulations under the Federal Clean Air Act.

Last time I looked (a few years ago), NAFTA trucks have to meet most of the same emission standards as Federal US trucks. That may not be as clean as a California-only truck, but it's not uncontrolled. In practice, the long-distance Mexican trucks are fairly new and hence emission-controlled, as are the Canadians and most large-fleet US trucks. Yes, some drayage immediately around border crossings uses older trucks, but with NAFTA implementation there's less need for them due to reduced transload activity near the border.

The assessment deals with all sources of air pollution near ports, not just trucks.