With cookie-stuffing the cookie is normally "generated" by loading a page in an invisible iframe. The loaded page is actually the same you would land on if you clicked normal advertising, with "everything on the page" - including an invisible gif. Visibility or Invisibility of the iframe doesn't change anything to the loading of this file. That's why it doesn't make sense to me.
Or did they use another method to place the cookie I don't know about?
The user might have received the one pixel "trap" cookie, but the article says they were watching to see users who only visited 1 page, since "normal" users click around and look at a few pages. If you only get the hidden pixel once, that's a sign you aren't normal.
It will be interesting to see how this goes in court since you cannot prove that any given single user was NOT a "real" user. But on the whole, the traffic smells wrong.
I don't understand why eBay didn't just ban the users when they suspected foul play. Trying to prove this criminally beyond a reasonable doubt would have been hard.
Or did they use another method to place the cookie I don't know about?