This is an example map made for TWHL user "Un_Nem".
Don't modify it first, just compile and see how the func_tracktrain starts. You will see that, although it was placed facing the wall, it will start in the normal position. The conclusion? If you place it normally in hammer but it spawns in the opposite direction in hl1, just rotate it. Yes, you can modify pitch yaw roll, but the fastest way is to actually "Ctrl+M" and rotate it in the opposite direction it spawns.
Also, take notice that the train will spawn with its center(defined by the origin brush) in the first stop target.