Sensitivity varies with the terrain. Feet become desensitised on rough surfaces, but sensitivity returns quickly on soft surfaces. Living heels are not like a bicycle seat, which wear out with use. Exercise stimulates growth, and thickens the cushioning. Secondly, if you are running hard and fast, you shouldn't be landing on your heels.
Heels are more for resting, than hard running.
My feet have a genetic problem, so I have to wear special shoes. Even those hurt. I have the same genetic problem. Our feet were not designed to be stuffed inside shoes. Try getting rid of the shoes.