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Just my take on this. I think a yacht owner has to register his yacht in his country of residence. Residence is defined by "centre of economic and social interest". So normally, someone living in Australia (owns or rents property there) and earning income in Australia (receives money for whatever reason or source there) clearly has both social and economic interest there - ergo must register his yacht in Australia. There is usually a 185 day rule, to complicate things but the owner's nationality does not actually play a role.
It gets complicated when the owner's social or economic interests differ from the normal situation. So an American might have a yacht built in Australia and export it to whereever his residence is. I think nominally, it can be US flagged and taxes paid immediately, if his residence is formally in the USA, but I see on this site that the USA has other rules for non-US citizens.
I suppose, a separate legal entity, like a company, can be formed in country X and formally be the owner of a yacht and take on country X's flag and taxes, no matter where the boat is built or who owns the company. Ships are often flagged this way.
The boat I currently have was first registered in the Channel Islands by a company formed specifically to own it. The company and the boat changed hands twice before the boat was imported into the EU and duties paid.
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