Roofs were painted almost universally by this time, and generally the same color as the sides and underframe. Paint is there to protect, so the structure would be painted. The roofwalks, that's a different thing. They were beaten to heck and easy to replace and paint was less important and possibly dangerous in terms of slips, though paint mixed with sand did get used for these on some railroads I believe.
All the cars on the ground at Sunset had seen tough service and neglect at high altitude for over a decade, all being somewhere around 15 years old by 1894. The UP was broke or close to it and the narrow gauges were being starved and neglected, especially the GSL&P. The ravages of freshets, snow, strong UV light at that altitude and just pure neglect, and paint that was hand-mixed, all contributed to a product that degenerated quicker than paints today. The roof paints fades more quickly than other parts of the body.
Dave Eggleston
Seattle, WA