It doesn't have to be a direct stand-in. It's mentioned in the article that people suspect McCarthy of reveling in the violence in his novels. Whether he does or does not he would certainly have been aware of that perception. Judge Holden as a character embodies many distasteful qualities of mankind, it would make sense that the qualities he embodies the most distinctly are the ones McCarthy sees in himself.

The only "self-insert" he's done is the main character of Suttree which is semi-autobiographical

The judge is an incarnation of evil and a pedophile so I don't think that's his Mary sue