I don't see any statement that it wasn't in the station. But that said, it's likely it wasn't: in other words he was probably found at a point where the train would have been moving. The station is in the center of town, with lots of car and foot traffic. The train blocks a street when it stops there, and the station area is well used as a parking lot.
He would have been on 5(13). It left Reno one minute late, then was ahead of schedule the rest of the way to Emeryville.
The fact that the train was never delayed indicates that he wasn't discovered, or at least linked to the train, until well after it left Truckee. That's unlikely at that station, although I suppose anything is possible.
Truckee is a long town – runs east to west more or less following I-80 (and the tracks). So it could have happened in an out of the way place within the city limits, i.e. within the Truckee PD's nominal jurisdiction. Otherwise the RGJ reporter would have called the Placer County sheriff's office, or Truckee PD would have referred him. Truckee PD would have initially responded, so more information is probably available on the watch commander's log (or whatever they call it in Truckee). The fire department would also have records.
Getting more info might require an in person visit to Truckee – unless you've established yourself with an agency, it's often hard for a reporter to get info over the phone. I know that from a previous career – it was true even decades ago, when cops and firefighters were more talkative. Truckee isn't in the RGJ's core coverage area, so given the understaffing of newsrooms these days, it's not worth the trip.
Truckee PD (and, by extension, Amtrak PD) appears convinced that whatever caused the injuries happened on the train, so there must be some evidence beyond "we found him by the tracks". Amtrak PD says "there’s nothing to suggest criminal intent". If they're saying that and there's any evidence at all, it's an indication that they're thinking in terms of some kind of accident or misadventure. Falling or jumping off a train, even at a relatively low speed, can cause severe injuries – the kind of injuries described.
The reporter wrote it as a human interest story – it's about the family, not the incident. Thirty or forty years ago we would have called it lazy reporting, but times have changed. Reporters don't have the time to spend tracking down facts anymore. It appears this story relied on three sources: a conversation with one family member who doesn't know anything about the incident itself, a brief phone call with a Truckee PD sergeant and an email from Amtrak.
Whether or not someone else was involved in the incident, the meagre information available does not point toward a crime.