>>...cranberries have a lot of quercetin in them
I hadn't known that. I know it's idiosyncratic, but this time of year (when raw cranberries are available) I usually keep a bowl out and snack on them (lots of taste, minimal glycemic load).
I mostly don't drink, but have not noticed more headaches (associated with alcohol or not) this time of year.
That said, I'd also suspect aldehydes. If someone has been consuming fructose, that has a metabolic pathway similar to that of ethanol. Even if it's impossible to build up enough quercetin to block aldehyde conversion and removal, at some point there'd be more aldehyde than could be promptly converted.
As a side note, I'd mention that I have the same doubts about metformin inhibiting the ETC - just around the concentrations needed to do that and typical therapeutic doses - but that's FAR off topic (sorry!)