Someone has legally purchased the shares for their account, yet the security was never delivered from one brokerage house to the other brokerage house because the person selling the stock never owned it or borrowed it in the first place. A regular short was pre-borrowed, so it actually existed. I'm not sure how they aggregate the numbers between a pre-borrowed actual existing share and a phantom share, but apparently naked shares do not show in anything except for the Fail to Deliver numbers, they never reach their destination clearing house/broker/MM.
Your also only looking at the 2005 rules, not the new amended rules.