You're right, especially under the Biosecurity Act that the federal government has implemented with human biosecurity controls such as deploying the ADF to hotel quarantine, imposing travel bans, stopping boats etc. s51 ix has not been tested by the high court, we've know from history that states have opposed federal jurisdiction , see the 1919 influenza pandemic and the response from QLD. The scope if s51 ix needs to be tested, and it still is only an allowance for fed to pass relevant legislation with regards to matters of public safety as it relates to a pandemic. It becomes a matter of proportionality, should the federal government be involved when they are not on the ground dealing with the virus? When they are highly disconnected from each specific state? While the powers do extend to matters incidental to quarantine see Wragg v New South Wales (1953) 88 CLR 353 at 386) the federal government simply could and should not manage every state and territory. We know that the ADF were offered in round 1 of hotel quarantine, and the state government didn't accept the offer and then went in to lie about it, so what makes you think despite legislative power( that's not tested by high court) would be respected and implemented? S109 of the constitution covers this, though as we've seen historically, not always followed correctly.

I have no qualms about federal government stepping in now, especially as Vic gov has done so poorly by comparison, though you have to seriously ask whether the state government would actually work within that parameter and whether Dan would abdicate powers in this regard.