And then there's the player movements that may have happened. Would the Storm have been able to retain Cronk, Inglis, Smith, Slater, Blair, Turner etc beyond say 2007? Maybe Cronk could've attracted a bigger offer from another club and left? What about Smith?
How much impact would that have a) on the Storm in those years, or b) the clubs that pick them up? Hell, Storm may not have even made the 8 let alone win the premiership in 2009...
Given the ultimate aim of every club is to win titles, taking those titles off the club made total sense. And unlike running/rowing etc, as you say, you can't just give it to who was runner up because it totally changed the complexion of the competition.
So yes, as far as the history books are concerned, there were no premiers in 2007 or 2009. It will record that Melbourne Storm won the Grand Final by whatever scorelines they were, but not that they won the premiership.