If the rear brakes were overheating, that would be due to the calipers not operating correctly. In other words they are sticking and holding pressur eon th epads even when you are not using the brakes.
There is no way that is NOT a warranty issue.
The pads and shoes wore out due to faulty caliper operation.
Nothing the driver could do would cause the rear calipers only to sieze up.
But I can understand them suggesting a "pro rata" adjustment to your cost.
basically, you paid for waht you would have used normally.
However, the main thing is, were the calipers overhauled?
If not, the same problem will occur again and more quickly.