Tennis Australia doesn't have any jurisdiction to allow/deny people entry to Australia. They have about as much authority to make such decisions as I do.
The reason why the medical exemption wasn't mentioned in the second appeal is the same reason the level select code for Sonic the Hedgehog wasn't mentioned (i.e. it was completely irrelevant to the decision at hand).
He also got an exemption from Victoria government - not federal governmnet but its not Tennis Australia saying you can come and Djokovic doing nothing else and ending up in Australia.
The reason it wasn't mentioned is because they abandoned that argument. The decision in both appeals were whether to deport him or not. They tried to deport him on the basis of his medical exemption and turned this into the huge story that *might* stoke anti-vaccine sentiment. They now go actually we are willing to accept the medical exemption. By extension surely you then accept he was wrongfully detained the first time around. But because of them turning it into this big story where Djokovic remaining *might* stoke anti-vaccine sentiment he has been kicked out of the country.
I said it was noteworthy they abandoned the argument during the 2nd appeal, not that the argument related to the new argument they adopted. If you are convinced the medical exemption wasn't valid, they could've announced intention to deport Djokovic for a 2nd time ASAP and persisted with that argument. Instead, they've effectively gone yeah we're willing to accept we wrongfully detained you before but the anti-vaccine sentiment that you remaining would cause (in no small part down to Australia detaining him and causing this story to blow up.) is why we'll deport you. (Also think its debatable that such sentiment isn't also a factor with him being deported)
If you are really worried about anti-vaccine sentiment, persisting with the medical exemption being invalid is surely a better tactic then accepting his medical exemption and that Djokovic "poses a negligible threat of infecting others". Unless you have doubts regarding the success of your medical exemption argument - which then goes back to them trying to deport him first time around
He might fake having Covid three weeks before again and not screw up in the aftermath next time.
He was kicked out the country because they argued him remaining in the country would stoke anti-vaccine sentiment. Lying about travelling in the 14 days prior, meeting people when he had Covid etc. not a good look but the argument relied on his past statements re vaccination and his perception.
Presuming France have their own rules allowing them to deport someone on 'public interest grounds' there is little stopping the French doing exactly the same as the Australian government did regardless of Djokovic's other actions.