The bin at Chama would have been filled the same way, from the end of the coal ramp. A gon could have been spotted there and left for as long as it took a crew to fill the bin without any need to interrupt coal deliveries to the towers.
Filling the bins wouldn't have been done often. The bin at Durango was about a quarter full as I recall in 1968, and it apparently wasn't taken down to allow for sand delivery until 1971.
The bin at Chama probably hasn't been filled to any significant capacity since the fifties.
The D&RGW was far more interested in keeping their operation efficient. I'm sure no thought was given at all to keep the bin at Durango. It had simply become an obstacle.