Passengers are a bit clever, they always choose the shortest mean to go the their desirate destination. For your example, the passenger will wait the second passage of the train in the C station to go to the D station. Does it answer to your question?
That's not what I ment. A1-B-C and A2-D-E are supposed to be different services; even if in real life they are operated by the same trains like in Carl's simulation, passengers won't consider that a single line and/or direct route, and won't be allowed to stay on board during the tecnical transfer between A1 and A2. A realistic passenger trip would be to take the first line to A1, use whater form of urban transit is available (or walk, since in Experimental there's this option) to go from A1 to A2, then board the second line to D.
Also, passengers to B or C are supposed to reach A1 to start their journey, instead (given my experience with Simutrans) in this configuration they could choose A2 or any other station of the second service as a valid starting point for a trip without transfers, while in real life that's definetly not the case.
I'm asking if Carl has a way to force passengers to make the proper journeys, since the simulation of the real network is the focus of the map, or if he just didn't care because that wasn't what he wanted to achieve. In the first case, I'd really love to know how he does it because it would be really handy for other games.
I'm afraid that I made this even less clear than the first post, but I can't explain it better. :\