The NCAA doesn't conduct a national championship in I-A football, and doesn't officially recognize a national champion. Thus, any championship awarded by any organization, including the BCS, is unofficial in any event. The AP championship is just as relevant as any other championship. I would say more relevant, in fact, because it's the one that's been around the longest.
http://www.ncaa.org/champadmin/ia_football_past_champs.html