The major theme of the film is awakening from a false consciousness. It’s an existentialist picture. This leaves it open to any of countless interpretations unrelated to gender. I think many more people have interpreted the film as Christian with Neo in the role of Jesus and with some of the names of characters and places having biblical themes. The film’s actual depiction of gender is rather conventional, including the action girl trope shown by the character Trinity.

Taken together, these two details make it very difficult to support the Wachowskis’ claim in the text. If anything, the opposite could be argued.