We don’t even understand friction. Which is one source of static charges, which we thus don’t understand well either. And static charges that somehow accumulate in the clouds cause lightning, which… I think you get the point.
As a child I saw an acted segment about ball lightning in childrens‘ TV, following a person around the house, and had nightmares for a long time afterwards. The thing is spooky as hell.
As long as you reject the hypothesis of "ionized matter" ball lightning is completely unexplainable. If you accept that ionized matter is hot and gives off plenty of EM radiation, it's pretty simple.