Aboriginal is "ab origio", literally "from/since the origin/beginning". Already the Romans used it in the sense of "there from the very beginning".

Indigenious is "indu gignere", "begot within". The "place" part is implicit. More of a "native" thing as in "natively born American" but the meaning shifted from the original Latin.

Practically, nowadays, they're synonymous. Over here we use "autochthon", literally "self earth/soil". Also used in geology and biology. The constitution speaks about "national minorities and ethnic groups", going by the last recent arrivals 600 years of living here as an ethnic group suffices for autochthone minority status. Though in our case there's no settler-colonials which of course changes the equation.