It's preference really.
Blocking the water straight off the pump before reaching the manifolds is ideal as there are no risks of water entering the cylinders via any pinhole leaks in the exhaust manifold. The only downside is that due to the location the valve is usually out of view and harder to reach with the risk of forgetting it closed and burning up your exhaust on your next day out after use.
The top exit will prevent water from back-filling the exhaust as well, but won't prevent water intake if there's any kind of leak in your exhaust manifolds. The upside is that the valves are easy to access and in clear view when doing any pre-flight inspections.
Hope this helps.