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.
But would Djokovic know the difference between the two before he got on the plane?
If I wanted to visit an event or a company in Australia I would presumably get a piece of paper with a crown at the top saying something to the effect of, "You're good to go, mate." Nobody's going to look past that piece of paper.
If one of the state governments is issuing pieces of paper on its own, then that looks like a real problem for the federal government to hash out with that state government.
If you want to make it the responsibility of every visitor to Australia to make the long distance phone calls to the authorities or to hire an immigration lawyer to study a piece of paper to ensure that it's legit, well, you're going to watch tourism to your country collapse overnight. Any internecine conflicts between the federal and state level simply can't be the problem of someone coming to your country to spend money (or in Djokovic's case, help raise it).