Hmm, I kinda trust Big Dave on this, but to pick up on one point in particular:
I highly doubt Alton Towers would have built the tunnel without a drainage system. I find it very hard to believe that the height of water could raise above the level of the tracks enough to stop a train traveling through. Would have to be atleast a 4ft deep puddle which would take one hell of a storm to create or a blocked drainage system for a good few weeks.
Think you've missed the point here. Bearing in mind how blinkin' deep the tunnel is, I would imagine that at the bottom it's below
the storm drains. Of course, water doesn't flow upwards, so I'd imagine* there'd be some sort of sump at the bottom for water to flow into, and a pump which would trigger once there's a certain depth of water.
All well and good, but given that this is an active rather than passive system, it'd have a greater chance of going wrong. Without a working pump, water level would rise and would have no where to go, so I can certainly see how it's possible for the tunnel to flood. Hence the water level sensor to warn if the level is too high.
* - this bit's speculative, but I'm fairly certain that the tunnel is going to be deeper than storm drains. Ergo, water would need to be removed somehow, so pump makes sense...