Such an amazing transformation

This actually can't really be avoided. It is more than likely demodectic mange and that kind is passed from mother to pup. He got treatment before he lost all his hair, so it may not be a case of neglect to the point you're thinking.

He probably had some type of mange or other skin infection

Most likely both and heart worms. This poor baby was on death's door.

It looks like demodectic mange, which is pretty common. Other than the hair loss, he doesn't look all that bad in the before pictures.