That particular twist might seem contrived, especially by today's standards, but Luke had a story arc. He didn't appear in the world as a perfect being. He made many mistakes and earned his redemption and victory.
Similarly, Harry Potter had a story arc. He began completely unskilled and naive. He made many mistakes on his journey to competence.
Both of these examples are the antithesis of the Mary Sue trope. It sounds like you're confirming that Aloy was born a Mary Sue, and didn't have to earn the mantle like any good story arc demands.
That particular twist might seem contrived, especially by today's standards, but Luke had a story arc. He didn't appear in the world as a perfect being. He made many mistakes and earned his redemption and victory.
Similarly, Harry Potter had a story arc. He began completely unskilled and naive. He made many mistakes on his journey to competence.
Both of these examples are the antithesis of the Mary Sue trope. It sounds like you're confirming that Aloy was born a Mary Sue, and didn't have to earn the mantle like any good story arc demands.