It has been ruthlessly coopted by people who want to see it that way and refuse to believe that any other interpretation could possibly exist.

I freely admit that the the fact that the writers and directors later both changed their gender makes a good case that that was an element of the story.

But, this was also a huge budget action movie produced by a mainstream Hollywood studio in 1999 when the world was far less trans-friendly than even today. There's no way they would have OK'd a movie that could only be interpreted as a trans allegory.