2003 Mercedes Benz S430 Clogged Cowl Drain and Damaged SAM

I recently left town for a few days, only to receive a call from my neighbor that all three brake lights were stuck on, which eventually drained the battery. Upon installing a new battery, there were a number of electrical malfunctions, including electrical clicking sounds, sunshades moving up automatically, no control over brake lights, etc. I brought the 2003 S430 into the dealer, and was told that the entire problem was caused by a clog in the "cowl drain" (sp?). There was no visible water inside the car, yet somehow the shop is saying that the water was able to get all the way to the back of the car, and short out the Signal Activation Module (SAM). I purchased an extended warranty with this CPO for exactly this purpose, but they are saying that it was my job to keep the cowl clear of debris. Could a clogged drain in the front of the car, with no visible water inside the car, reach all the way back to the rear of the car to damage the SAM?