I was watching a rebroadcast of "A Chef's Life" S4 E8 "All Sunchoked Up" with Vivian Howard today. She addresses this issue. If the chokes do not get hit with several hard frosts, the flatulence factor renders them, if not inedible, extremely regrettable. It's been too unseasonably warm, at least here, for them to become something one wants to eat in polite company right now.
Sorry I couldn't provide a link. It seems UNC PBS has become much less generous with their free episodes of the show now that her book has taken off so solidly.
But yeah, you're right about folks gut bacteria. If they are not used to eating much fiber, certain things can be er... problematic.
There is a funny account from Kerry Beal on here somewhere about regretting eating sunchokes and hanging out outside while on a shift at a hospital or clinic. I doubt she will be a fan and future consumer of even properly frosted ones. If you're not growing these sunflower related tubers yourself or from a trusted farmer, it's probably not worth the risk.
It makes me wonder if short stints in the freezer alternated with fridge visits could render grocery store ones flatulently harmless?
