I can only speak from looking at rego/duty options for myself when importing a US built boat to AUS, NO EU involvement and this is not professional advice.
My first and only informed advice is to go to a professional in this field.
If you plan on keeping it the EU for 2-3 years, I can see no value in an Australian registration at this time. The EU taxes
are paid, take advantage of them.
Whether it's best to have German or some other EU flag/rego, I'm not qualified to say.
In three years it will have depreciated, get a survey
done that reflects this lower market value immediately before you transfer to Australian registration and import
the boat here. You will be taxed on that amount, a lower value is in your favour.
If you take longer than one year, from that valuation, to physically get the boat here and import
it, you may well be forced to have it re-valued, you may not like the result.
If it is not in your plans to import the boat to Australia then of course just sail under your EU rego.
I think I got that right but please check the EU options out with some authority there.
The Australian regulations
are available online, possibly from AMSA, search for "importing a boat to Australia".