Tesla has sold 5 million cars. I think a good proportion of those will have been driven in heavy rain at some point. If this was a common problem someone would have some stats.
Speculation: I suspect somewhere inside the car they have markers that let the engineers know whether the car has been submerged. If those markers have tripped then you're out of warranty.
Because they claim the battery is waterproof, and surely, if driver actions were reckless enough to pierce the battery seal, they can show how it happened.
After all, the CEO advertises the car as almost-a-boat.
Speculation: I suspect somewhere inside the car they have markers that let the engineers know whether the car has been submerged. If those markers have tripped then you're out of warranty.