Superman's super powers had purely naturalistic explanations. His powers existed only relative to the unique physical properties of our particular solar system.
Even given (or ESPECIALLY with) evolution and strict materialism, there is no reason to think that there might not be somewhere in the universe creatures that have evolved with physical properties that would manifest differently in our own system. A very easy way to see such a possibility displayed is to consider how it is on the moon. With the weaker gravitational pull, we'd be able to jump higher, in theory, than a native.
Basically when you are allowed to postulate even the most ridiculous physical processes, and slap it with credibility if you think you have billions of years with, then any possibility exists. Indeed, we should even say its probable!