Usually SVO (or SOV for object pronouns) is the standard word order, but in certain contexts the topic-comment-distinction (the relevant/new information is placed at the end of a sentence) overrides SVO/SOV.
Here that makes sense, as:
"Głowa mnie boli." (głowa is the topic, boli is the comment) - technically answers the question: "How is your head doing?" But if such a question were to be asked, then głowa would be redundant. Just "Boli." would be enough.
"Boli mnie głowa." (boli is the topic, głowa is the comment) - answers the question: "Where do you feel pain?"
Having said that, Głowa mnie boli is of course correct and accepted in the reverse exercise.
I guess it's a colloquialism then, or a Ukraine dialect. I've heard it my whole life. There is a huge Russian-speaking community here in Los Angeles, and a lot of us of my generation of immigration are from Ukraine. Since Ukrainian is much closer to Polish, this could be a Ukrainianism in our dialect of Russian. But I've heard мне болит, ей болит, ему болит, тебе болит, etc., spoken my whole life, to say that something hurts. So the Russian National Corpus can suck it.