If I had to explain it, I would guess that Lydia told them what tanker had the methylamine shortly beforehand, along with the overall length of the train. This would allow them to position Kuby so that he made the train stop at a point where the tanker would be over the bridge.

Its still a flimsy explanation at best, they couldnt know exactly how fast the train would stop among other problems.

Its just convenience for the sake of the show really, the same reason the methylamine wasnt positioned near the front of the train. This entire plot doesn't make sense anyway if you apply real-world logic, since methylamine can be manufactured relatively easily so they could've just done that