Why should he deny it? He was all over the international press within hours of the event - do you think that if he were an eyewitness or somehow directly connected that he would not have mentioned or confirmed it?
Aside from the fact that I know there was only one source for the claim, other things that make me suspicious include the fact that the reports do not agree on the airline the supposed 747 belonged to (some say AF, others JAL), as well as the fact that none agree on how close F-BTSC came to the supposed 747. As I said before - variations on the story include F-BTSC passing within 7m, 70m or 7 yards(!) of the alleged Chirac 747, the alleged 747 itself either on the runway and exiting, at a holding point or *actually crossing the runway across F-BTSC's path*. Some even have Chirac himself "looking on in horror" as the flaming Concorde passed by.