I understand the concern. I suspect water is as much or more of a concern than impacts from below. The counterpoint is the 20 gallons of gasoline that seems to be okay down there with nothing more than a plastic rock deflector in most models. It's equally vulnerable. And the actual size is marginally larger than two 12v batteries. They could just go under the hood to keep them protected and relocate the controller to underneath or inside the cabin.
Another thought - odd as it may be - there might be a future where people try to steal them like catalytic converters.
All of those issues seem pretty solvable with relatively small engineering work. Protect them with skid plates. Seal the case for water and vent to an appropriate level or entirely seal them and use active or passive liquid cooling if necessary. Or even just make the case flat so it only raises the rear deck 2 inches instead of the shape of a brick sitting in the middle.
Another place they could go is under the drivers and passenger front seats. That's almost always unused space and those seats never need to fold down.
