But if both players are moving across rough terrain and have a road leading to a shared secondary resource, the encounter could happen very quickly.
So what? Both players reached the shared secondary resource; it will just result in an early Fort Battle, possibly the first one. Someone might retreat or buy their way out. In my opinion, this would actually be more interesting. The player who wins the first Fort Battle is unlikely to continue the attack; it's unlikely they'll finish the job in the castle, and the second week is coming up soon, giving the opponent time to recover. Plus, after this, the players will likely go back to gathering resources. On the shared secondary resource, a war of scouts will begin, or some other scenario. Why would you want to reset that?