Also consider that endogenous alcohol is brewed up in the gut, it then travels directly to the liver where a significant amount is metabolised in the "first pass" effect. Plenty of alcohol dehydrogenase in the gut wall too. I'd be surprised if much of the low level of alcohol found in gut-fermentation got through the liver, but that's just my supposition.
This unfortunate effect can be avoided quite nicely by swilling a strong whisky around in your mouth without swallowing it. You get a nice buzz as the alcohol goes direct from the mouth to the heart to the brain. More of a student trick, now one can afford to swallow and take the loss
Anyway, even if the pilot claims he is over the limit because of endogenous alcohol he is still over the limit and so unfit to fly. If he claims to be one of the rare people who may truly be affected by endogenous alcohol, I think that would be as medically disqualifying as being epileptic.