As far as I know, there is no question that Bonin was suitably qualified. It is covered by both the BEA report and by various contributors to these threads who included both present and retired airline captains.
What I and others have wondered, to which it is unlikely that any answer will ever be forthcoming, is why the commander left it until he was about to depart from the cockpit for his rest period before he sought confirmation from Bonin that the latter was indeed so qualified.
Unless somebody has evidence to directly challenge the investigation into licensing that BEA conducted, there appears to be really no reason to continue to cast doubt on this.