The problem is not Peragrine himself. The problem is in everything around him. To accept them as the same person would mean we accept the events and background stories of I.I. as canon for the KotOS Universe. That means the manner of the Darkitect's death, a second Jonna, the existence of the cube, Jonna's concept of Mythrans/First Builders, Jonna's concept of Typhonus would all be considered part of the KotOS Universe. If these are not impossible to include, they would at least be hard to and limiting.