I can see what the agent's argument is - whether it is valid , I am unsure
The passenger's journey was actually a r/t to PVG with just a connection back to origin at NRT
LAX-PVG , PVG-LAX via NRT. Given that LAX-PVG is further than LAX-NRT, it is a r/t to PVG and not a transit onwards to Tokyo
With a 90 minute transit, the passenger is not destined for that 3rd country and will not clear immigration, customs etc