Personally, I'm glad COMC doesn't reject this sort of material... I just wish they'd deviate from beckett sometimes and not list this kind of stuff under the regular card's listing. Or at the very least make a note on each an every one (which I think they try to do if they catch the issue on listing).
There is definitely a market for these kinds of variations regardless of how they ended up on the secondary market. What the true values are is up to the buyers/sellers, but COMC seems like an ideal place for oddball items like this to be featured.
Now if the cards are unquestionably tampered with (e.g. Fleer bankruptcy empty window logoman cards that have had bogus logomen inserted, counterfeit cards, forged signatures, etc) then that kind of stuff needs to be weeded out. Otherwise, let the market decide what may or may not sell... but do everything possible to let the buyer know if they are getting something different from the beckett listing.
On a related note, another reason to not disallow items like this outright would be a card I just listed:
2000 Topps 20th Century Best Sequential #CB5 - R.Henderson SB/1334 - CheckOutMyCards.com
The card is supposed to be numbered, but isn't. But thats the way it came out of the pack. Its simply a factory error. Some buyers might not want it. Some may want it but not want to pay as much as a numbered version. Some might want it and be willing to pay a premium for its uniqueness. I'm fine paying 1 cent a month to let things play out with the card, and see what kind of market there is for it. Better than sitting on my desk at home with me wondering what to do with it.