Hmmmmm, I am not really sure that "person vs. supernatural" is actually a good description of the conflict in this book; however, I will do my best to help you answer the question. The reason why I feel that way is because the only semblance of a supernatural presence is the imagination that exists between Kevin and Max.
It is this imagination (that of Freak the Mighty, that IS Kevin and Max) that allows the two to have many adventures and much fun together. It is Kevin, especially, who is good at imagination.
Pain is just a state of mind. You can think your way out of everything, even pain.
There is an adventure when the two "fight dragons." There is an adventure when the two enter the hospital's research ward in order to discover the robotic bodies that one day will belong to Kevin so that he can get around better due to his disability. There is the "real" adventure where Kevin tries to rescue Max by threatening with a squirt gun that he claims is filled with acid (but is actually a soap and spice mixture).
In short, I think the best answer to your question would involve Max's violent family members vs. Kevin's vivid, supernatural imagination. That is a true conflict, especially in the case of Kevin squirting Kenny in the eyes with the burning spice and soap mixture! This is truly a conflict; however, it can't really claim to be "supernatural" because it has nothing to do with ghosts or spirits or any other anti-natural phenomena.