Originally we wanted to replicate the ideal look of metro maps and didn't allow lines to cross at all. However this hard limit on what the player could do wasn't very enjoyable when learning the game, and also wasn't quite realistic as many maps have to show lines crossing each other. So a year or so ago we loosened the restriction to let players cross lines, but with the soft penalty of having trains slow down when crossing. This means that you can do it if you have to but it leaves room for optimisation.
It makes more sense if you think about Mini Metro as a map simulator, rather than a metro simulator!