As somone who has conducted a fair amount research on the history on the WP/CP/SP line through Niles Canyon now operated by the PLA, I can tell you that John Sweetser is correct, and that there is no controversy whatsoever. I have inventoried every structure along the Niles Canyon Railway from Niles to Pleasanton.

I will add that the lettered structures were not only used for culverts. Every structure on the track recieved a letter including bridges, culverts, cattle guards, tunnels, and some grade crossings. Buildings along the tracks were not included. The letters were always sequential, and sometimes changed when structures were added or removed.

All of the stuff along the rail lines had be tracked and easily located. Operating personnel and section crews might not be able to remember something like "Bridge at milepost 31.57," but "Bridge 31D" was easier. I do not know when this system was implemented or when it was discontinued.