G'Day Paul, and welcome to CF.
I think that you have little choice here -- as a non-Australian citizen you may not document your new vessel as an Australian ship. If you want to leave the country, an Australian state rego will not satisfy Customs
. Therefore, it seems that you must document her in your country of citizenship, or in some "flag of convenience" nation. The latter is probably not appropriate for private vessels.
And until the vessel is complete, it will not require any rego at all!