To me it sounds like you’re making it more complicated than it needs to be. It’s a game, not a simulation of shipping per se.
As Yeol said, it’s hard to understand this 100% without seeing the issue. From what I gathered, you’d probably want to skip the cargo station next to the other cargo station in city B. When the ore is unloaded it will take the fastest route to a destination where it belongs. Since this ore is so far away in the first place, you’re better off making a long line either by using trucks or trains.
Two shorter trains makes for a faster cycle than one long train, and it becomes more attractive for the ore mine to use a line with shorter waiting and transit time.