There were a few suspicions on the legitimacy of Joan II because her mother had commited adultery. If Joan is born John, I guess Philippe of Poitiers could try to use that argument to have himself proclaimed King. However, I don't think that would be very successful because baby John would have the same supports as he had as female OTL, most notably the Duke of Burgundy, Charles of La Marche (OTL Charles IV of France) and a few other great nobles. In fact, it's possible that TTL John I would get even more support than OTL Joan II which would be troublesome for Philippe.
Plus, Philippe could be satisfied enough with the Regency: he got it while Clemence of Hungary was still pregnant with OTL John I. Here, he would probably also obtain it for his 4 year old nephew. And if he really wants the crown, he could just poison his nephew: it's a dark rumor with no proof (exploited a bit by Maurice Druon in The Accursed Kings), but he is suspected of having OTL John I poisonned so that he could become King.
Wonder who TTL John I would marry though if he is to live up to adulthood. Maybe Philippe of Poitiers' eldest daughter? That way, he would get the Counties of Burgundy (Franche-Comté) and Artois.