The association of terms like “native” and “aboriginal” became associated with unsophisticated and savage because of the prevalent ethnocentrism of the Imperial age (primarily 16th to 18th century European history, however may be considered to extend into 19th to early 20th century European and USA history).
Whether calling them aborigines, natives, or savages; the prevalent rationale was that the cultural, scientific, industrial, legal and social achievements of Continental Europe exemplified the highest achievements of humanity. This engendered a discriminatory attitude to those societies that function without these same advancements.
I believe history shows that the “enlightened” could be judge at least as “savage”, if not more, than any culture they judged; consider the Slave Trade, the Trail of Tear, and the destruction of South American cultures (Maya, Inca, Aztec) by Spanish conquistadors, the subjugation of India, the subjugation of Vietnam, the subdivision of the entire African continent, etc.
However “aboriginal” in its own primary definition is more akin to “native”, rather than the engender “savage”.
Referring to the etymology, the Latin root really implies just the original inhabitants.