Nobody is asking for that, and nobody thinks that kind of thing would solve the problems in indigenous communities, or that it would be desirable. Indigenous people want to be able to participate in mainstream Australian life, but feel adequately represented and heard by the political system and broader society.

Also it's been done before https://en.wikipedia.org/wiki/Aboriginal_reserve

I don't understand how autonomy and apartheid are anything other than positive and negative spin on the same concept.

To use a marriage analogy, autonomy (bounded) is consensual separation where the injured party has initiative and control over their actions. Apartheid would be the husband restricting the wife to a certain area of the house and beating her everyday.

Autonomy is the best way to preserve culture. A tiny minority living among people who do not share their values will eventually lose any connection to their past due to assimilation unless they adopt extreme orthodoxy like the Amish/Mennonites/Haredim (who too have to form ghettos to achieve their goals).