It could be an old Reading box too, but this does look like something a shortline would have used. Generally Reading stuff this old would have a PRR mark instead for Philadelphia & Reading, the old name. Caboose toolbox would be my bet. They had to carry a set of tools on a freight train and the ones not meant for use on the engine itself were kept in the caboose. Most railroad utility boxes would have side handles but not all tool chests did.
You haven't shown the tray. It's typical of these chests to have one. If it looks newer, maybe a replacement rather than an added feature? Edit. Oops just spotted the pic of the tray. Looks original to me. Why do you think it's later?
Any sign of handles on the side. I would say a toolbox but no handles would make it awkward. He may have had his initials on the bottom.