Absolutely. Lara Croft is not a Mary Sue. Poorly fleshed out, an stereotypical teenage boy sexual fantasy and one dimensional, no doubt, but it’s not like the computer programmer who came out with the concept considered her his embodiment in an universe he wished he was inhabiting.
It’s not even any self-insert in a story. The narrator in “Breakfast at Tiffany’s” may be a thinly-disguised version of Capote, that doesn’t mean his path follows the idea of a masturbatory wish fulfillment fantasy the path of a Mary Sue story does, for instance.
Maybe it’s not the term Mary Sue what’s wrong here, but it’s overuse.