Well, unfortunately agents are often not that well informed, as you have experienced. They're good for quoting prices and selling tickets. For anything else, well, a large grain of salt should be applied.

What the agent said about train delays/interruptions is partly correct and partly incorrect.

A train can be partly "bustituted" for all or part of its journey, a relatively common scenario would be a major freight train derailment that blocks a line. Amtrak trains are stopped at some place on either side of it. Amtrak will frequently charter buses to take passengers between the stopped trains, turn the trains around and the passengers continue their journeys on the turned around trains. In that scenario the agent is wrong, the bus bridge and the continued journey on another trainset wouldn't use up any additional segments.

Another scenario is rerouting in case of a delayed train. A fairly common one is the Southwest Chief or Sunset Limited mis-connecting with the Coast Starlight at Los Angeles. Passengers for the Bay Area and points north are usually rerouted onto the San Joaquin from Bakersfield to northern California and its regular bus connections from LA to Bakersfield to catch up with the Starlight. If you were going to Seattle, Amtrak would reissue your single Starlight ticket as Thruway bus ticket, a San Joaquin ticket and a Starlight ticket, consuming two additional segments. In that scenario, the agent would be correct.

The key factor is whether or not tickets have to be reissued for multiple services. In the bus bridge case they aren't, in the Chief to Starlight miss, they are.