"I normally get a lot of questions regarding native U.S. identification, and I like to be as thorough as possible. But this whole mess has got me at a stand still. Which genus is most commonly accepted now for North American Ratsnakes?"

"Most commonly accepted" is a difficult thing to evaluate. IMO, it's clear that Pantherophis is the right name, though, and that retention of Elaphe tends to obscure present knowledge.

"Has the DNA really proven the Pituophis placement?"

Unequivocally no. Different analyses (i.e., maximum parsimony, maximum likelihood, and Bayesian) of the same data give different results (as evident for MP & ML in the publication by Burbrink & Lawson, although they do not discuss this at all), and no analyses give strong support. Neither monophyly of either genus nor relationship of each to other members of tribe Lampropeltini is resolved at this point.

I've got a very brief submission to Molecular Phylogenetics & Evolution (the same journal that published Burbrink & Lawson's study) on this point. I should hear soon whether or not it has been accepted for publication.

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