For DEN>SJC this afternoon the one-way coach fare was $303 on a day that the itinerary was available. Other days (example = Nov 3rd) showed no trains available.
I was able to find DEN>EMY as operating on the days that DEN>SJC said no trains.
Breaking it into DEN>EMY $103 and EMY>SJC $19 made it more reasonable, although then they wouldn't have to worry about Train 5 connecting to the last train to San Jose. Perhaps they've rolled the cost to them of a hotel room in EMY into the fare.