I would just like to add that goods wagons and vans became 'common owner' during WW2 so could be seen far from their normal habitat (although of course company-owned vehicles were never confined to their own company's area). The same applied to private owner wagons.
Repairs and repainting were quite basic. Passenger trains could be much longer than in peace-time, especially when troop movements were involved. At night, a blackout was in force and every effort was made to conceal light coming from, for example, the fires necessary on steam engines - tarpaulins could be used to conceal light from cabs. I believe too that signal lamps were shrouded to conceal them from aircraft.
However ( and this was mentioned in a recent TV broadcast) railways were used extensively as navigation aids by British pilots, especially those (often women) delivering new aircraft to airfields.
Where the risk of enemy landings was considered possible, there were often large concrete blocks by the side of railway lines; these were to prevent the movement of tanks. Similar blocks were used on roads - there were some outside my own school (in fact one was built in a hole made in the school's perimeter wall) and in the case of roads at least these were supplemented by lengths of rail bent into an inverted V shape, to be inserted in holes in the road between the concrete blocks.
Another 'scenic item' along the railway would have been 'pillboxes', small fortress buildings of brick and concrete with firing slots, often to be used in case of need by 'Dad's Army' - in my boyhood, this was certainly a true description, as my father's sten gun lived in the umbrella stand in the hall (although the ammo was kept elsewhere).
A fully scenic wartime route in Trainz would be interesting - at least, there would be no need to provide nightmode in buildings! But the glow in the sky from FIDO* which could be seen from our house would have to be provided!
*FIDO - Fog Investigation Dispersal Of - fuel burned at airfields to disperse fog at night. In our case, this was at RAF Marham which (from memory - and a visit) was a Lancaster base.
Ray