Receiving a CGC label back with a raw card does not mean the card is authentic. In fact, we send back labels that say NG (Not Genuine) all the time. These labels of course could not be used again as they are printed with the card information that is tied to our internal database.
The only way in which CGC guarantees the authenticity of a card is if it is still sealed in its original CGC holder. If a card is returned raw, like these were, we are not making any claims as to the authenticity of the cards. Could they still be authentic? Of course, and I am sure they are. But because they were cut in a way that can be seen as deceptive, we will never put them in a CGC holder. There is no room for debate on this. We simply will not be doing it because, intentional or not, they are made to look like a different issue.
As for the inking issue that was brought up, inking to hide wear is of course deceptive, but it is not done in order to alter the card to make it into a more valuable type; but rather to appear to be a higher grade. That is why those will still be graded as if the inking wasn't there, but they will go into a Green Qualified label with the issue noted on the back.
A similar example would be a fake 1st edition stamp added to a Pokémon card. Even though it might have the same amount of additional ink applied as a card that is inked to hide wear does, its the attempt to make it into a different card altogether that is the main issue. That too would be returned as altered.
Thank you,
Paul