It was quite common to have multiple baggage cars on the San Juan. If you dig through the old books or the WEB for examples of San Juan Consists, multiple baggage cars happened a lot. Typically the passenger count would drop to requiring only one coach and a Parlor Car during the winter months. Two coaches, or more, were more common in the summer months.
There are some great photos and videos of San Juan's with open platform coaches tacked on here or there. Sometime on the end, and sometimes in the middle of the train. ( And not just the Chili Train cars from Alamosa to Antonito, where they would separate for the trip to Santa Fe. I mean all the way to Durango. The odd ball stuff is fun to find....
Kevin