Indeed, the crackpots are out on the Piri Reis (the extraterrestrial crowd for one), so it's understandable if you would walk away with the impression that it's junk science. But, it seems real.
Of course the really intriguing aspect of the Map is the representation of the Antarctic landmass -- without the icepack. Not sure what to make of that. It could just be that the map does not claim to represent an accurate gridline representation of a coastline, but is a "portulano" map that gives bearings & distances from port-to-port.