That's true for Project 2501, but not the cyborg protagonists of Section 9. They aren't Frankenstein's monsters, especially not in a society where some degree of augmentation is so normal.

That includes Motoko Kusanagi--even when it's been hinted she has relied on artificial bodies since childhood, that's still a very human form of alienation.

Agree on that, but my point is still that GitS isn't a good example because cybernetics are there because of setting, not necessary the "modern Prometheus" thingy.

GiTS creator Masamune Shirow's earlier works also feature androids or other sorts of synthetic life. Particularly Buaku's gang and Crolis in Dominion, and the military androids in Black Magic M-66.