Earlier this year, Kofax acquired Nuance Document Imaging, a division of Nuance Communications, Inc. My guess is Kofax and Nuance PDF software are basically the same, just branding changes (there may have also been a licensing relationship before the acquisition).
PDFPen and PDFPenPro do contain licensed Nuance-Omnipage OCR software, Omnipage is a part of what Kofax acquired. I think that’s the only connection, PDFPen & PDFPenPro are made by SmileOnMyMac. It seems almost everything commercial that does document OCR either uses code from Omnipage or ABBYY Finereader.
You can compare PDFpen and PDFpenPro, both have OCR but only Pro has “batch OCR” and a few other features.