I don't remember ever seeing any flat car deck (from any RR) that
wasn't "weathered wood" (grey+brown tones) in color ... both in
real life and in photos.
Although it is certainly possible that some RRs painted the decks
when new/delivered ... I would be surprised to learn that they ever
re-painted and would expect the deck to loose all traces of paint
very quickly. But what do I know?
My process for 'coloring' flat car decks involves a base coat of
grey that is then dry brushed with a fine brush and a variety of
different color streaks applied in random - the majority of those
streaks are different shades of grey with a very few any shade
of brown. These 'colors' are often thinned out to a wash for
this one, then thicker for the next, etc.
The final step, as is my usual practice for all weathering,
is to airbrush a Very light 'dusting coat' of some weathering color
or other (grey/charcoal/tuscan/what ever). This last step "blends"
the overall car colors and makes it hard to see the brush strokes or
washes as separate colors.