Ross's comment is closer to current reality than Devil's Advocate's. If you've got a clean source (and the Pathfinder ePubs qualify as clean), then Calibre conversion works just fine for personal use. The old problems Devil's Advocate mentions are just that. Old.
That said, however, Devil's Advocate's second bit of advice is accurate. If you are on a tablet that has apps that can read both file types, then it's always better to read in the original format if you can.