The additional taxes are due once you are not a "transit" passenger, which is defined based on whether you pass through immigration or not.
Technically for an overnight stay you don't need to pass through immigration (unlike most Australian airport, MEL is open 24x7), however there is a legal requirement to have a visa or similar (eTA) if you are in transit for more than 8 hours, so I'm presuming AS is probably using either the "overnight" or "8 hours" as their criteria for whether these taxes are due or not.
If you are intending to pass through immigration then the story is clear - the higher taxes are correct. If you're planning to remain airside then you might have a claim regarding being overcharged, but I wouldn't necessarily like your chances...