I was trying to think through things like that, but if that were the case, the second ("sideboarded") list wouldn't have maindeck copies listed. For instance, look at Tendrils of Corruption's appearance in the second list (#42) with 12 maindeck and 19 sideboard copies, and its #20 appearance on the first list with 142 MD and 17 SB copies.
My new best guess is that the first list includes all instances where a deck has a majority of the copies of a card in the maindeck, and the second list is whenever more copies are sideboarded than maindecked. So a deck with 3 Damnation MD 1 SB would add to the first list's total, but a deck with 1 MD and 3 SB copies will add to the second list. If they're even (infrequent, but a 2-2 or 1-1 split does happen I guess), I assume they must add to the first list, because the maindeck is bigger. That sure is confusing, though.
Either way, as long as the lists don't double-count each other's contents, my analysis should be valid. If anyone knows for real, I'd still love to hear about it.
