I just can't bring myself to believe that Audrey could raise Frank 2.0. Audrey seems like too good of a person to put up with even an ounce of that sort of behavior. I'm thinking he's either Jerry's kid or, somewhere along the line, Ben had yet another illegitimate child (a tad far-fetched with his "moral rehabilitation" in late season 2, but nothing's impossible).
This is Twin Peaks we are discussing. A location where evil literally manifests itself. Drugs, abandonment, and a plethora of instances can cause any child to fly off of the behavioral rails, regardless of how brilliant anyone's parenting might be. I don't think we should rule out Audrey as his parent. Audrey could be the mother and also not "raised Frank 2.0", because her upbringing of the child might have little to no consequence on how the kid turns out, especially if his father is Mr. C. like many are starting to believe after the Doc Haywood soon.