He's flying around the world to play in a tennis tournament and he ran into a game of Rock, Paper, Scissors that he neither expected nor wanted.
To a great extent I agree with you - I originally thought Djokovic had been either disingenuous or very careless in accepting the documentation from Tennis Australia (in concert with the Victorian government) as valid, but I now accept he had genuine reason for making that assumption.
But I would like to point out, it's not quite as you describe - this is not a matter of someone from a different part of Australia swooping in. This is a matter of the Commonwealth government of Australia which clearly and unambiguously has constitutional authority over entry to Australia, stepping in over a state government (that of Victoria) that has no constitutional authority whatsoever in this area.
It is extremely problematic constitutionally speaking that a Judge has allowed a decision by a state government to determine who can enter Australia, over the objections of the Commonwealth government and that is basically what has happened here. Djokovic isn't any threat to Australia - but the Victorian government has a history of cozying up to China, and of being soft on illegal immigration (they can afford to be - hardly any illegal immigrants try to enter via Victoria). If they can now issue permission for entry, we have real security issues.