.beacon 21 needs to be added everywhere the intensity of rain changes, so you need to place them for every bridge and tunnel in the route. You need to do the same for the cab brightness commands and the fog commands. Fortunately, the way Tony has constructed the NWM routefiles means that you can copy from an existing one.
Have a look towards the end of one the rainy NWM route files. All the .fog, .brightness and .beacon 21 statements are placed together at the end of the file, which means that you can copy and paste the entire environment setup to change the conditions (apart from any change in the ambient lighting at the start of the route file). So if you want to make a route rainy, just edit in the environment section from an existing rainy route over the same section of track* (doesn't matter if it goes slightly further).
*This can't be done easily if either route includes a reversal as the distance markers in these routes don't always match up with the standard routes.