When I first rode the "Silverton" as well as other standard gauge passenger trains in Colorado in the early 1960's, there were no holding tanks as the ROW was the holding tank. Signs in the restrooms always asked "please do not flush while train is in the station" or something like that.
I do not recall seeing a "honey wagon" in Durango until the early to mid 1970's. At that time, the DRGW used the honey wagon to empty the tanks after the trains were parked for the night in front of the depot. The D&S changed operations in 1981 and we soon had a stationary dumping station on the balloon loop and the train was spotted to empty the tanks. The cars that still had coal stoves (which the D&S added and expanded in 1981) were serviced by the coach cleaners by filling up 5 gallon buckets at the coal pile. The fires were maintained by security during the night. It wasn't until later years that the stoves were removed and propane (RV) heaters were installed. Ice and water were basic and I believe they were loaded at either the coach yard or the depot tracks...or both.
While at the Grand Canyon Railway and when restoring the ex SP Commuter Cars, holding tanks had to be installed as they never carried them during their service life on the SP.
MD Ramsey