This isn't what happened in my latest game, though it might be due to peculiarities in the continent I wound up with. Unfortunately, I don't have a before and after savegame. In any case, my continent was a really oddball one, with two horizontal regions each extending about 1/3 of the circumference of the globe running near the north and south poles, and a long vertical landmass joining the two. Overall sort of a distorted S-shape or logistic curve. The Via Appia worked as expected, but the Golden Spike's railroad ended in two seemingly random locations. I want to say that the western branch went about halfway down the length of the western horizontal region, while the eastern one only extended about as far as the eastern edge of the vertical region. I did make use of forts and strategically placed cities to create canals through a few narrower regions of the continent though.
Would it make it work better or more consistently if it searched for easternmost and westernmost cities instead of points?