The courts decided they have jurisdiction over Aboriginal people because Cook discovered Australia under First Discovery. This is clear when analysing the details of landmark cases in early criminal case law – summarised in the image below (this is a photoshopped adaptation of Davey’s proclamation of the same era);
Under First Discovery principles, the discovering Crown has a duty (fiduciary duty) to protect the rights and interests of the people of the discovered land. This duty was used by the courts as a hook to pass laws regarding Aboriginal people.
The duty only applies to areas of First Discovery, hence why in Bonjon – a case in Port Phillip which is outside of Cook’s First Discovery claim – the court did not decide on jurisdiction, shrugged their shoulders and handed Bonjon over to the “protector”.
Most of “Australia” was acquired by the British through a “settlement” (as in a legal settlement/agreement) with the Dutch. The settlement was concluded with respect to native inhabitants (article 14 in the treaty) in 1830, hence why the courts walked away from R v Murrell, which was before this date.
First Discovery does not apply over most of Australia. It only applies in pacific flowing water catchments (and historically appeared to apply to the Murray Darling basin). There is no Crown fiduciary duty over most of Australia.
This was confirmed in the Hindmarsh Island case where the courts decided they can pass discriminatory laws against our interests.
This means that unlike other peoples under settler colonial subjugation who have had fiduciary duty recognised and had at minimum lip service paid to it – we have not. Crown conversely has no right of preemption. This means we can treaty with literally any nation in the world. We owe the Crown nothing.