Gary
Consider this theory/musing/waffling Peter.... TS is running with the security permissions of the logged on user--said user doesn't have the necessary permissions to view that folders contents--therefore neither does TS. TS can't ask for elevated permissions because as far as Windows is concerned it's just a sub-routine of Steam. As you've said, if Windows doesn't know about the route it doesn't exist.
Running as administrator and/or disabling UAC could get around that I guess??
Good points but I don't believe that Windows is that specific

.
It would be too complicated, too many rules to follow, Windows is pretty universal when loading stuff into the VAS and it is more worried by exe files and the like. My belief that loading the menus screen is an internal process in TS2015 and the security is predominantly about railworks.exe.
In Procmon as Railway.exe is loading the menu screens none of the route folders seem to be accessed, so the menu icon (which as I understand it is the missing item???) may not be subject to any Windows security at that point.
The specific route only seems to be accessed when you select it with a scenario, editor, etc.
Me personally, I like plain old vanilla waffles!!
pH