if I did the same timed route between Paddington and Reading for example over and over again would the signals always be the same or do they randomly change each play through?
It depends on your driving in that case. Since the amount of traffic on the route is fixed, you can expect the same signals for the same service. Only if you are too fast or slow it could change. So if there´s a train in front of you and you are faster than the game wants you to be you will get yellows and eventually a red signal. It does vary between certain services, always depending on how much trains are on the route infront of you.
The signals work on a block system giving you a clear to proceed if the section in front of you is free. So as xD 2Bad4You says it depends on what's on the track ahead of you. So given that the AI runs to set times if you always start at the same time and travel at the same speed the signals will remain the same. You can on some services vary this by starting later. For example try the HST service 1K34 by first departing on time and then again leaving 2.5 minutes late at 8:21.30. The signals are quite different!