Do you think that The Matrix is about transgenders for real or maybe it's just to generate buzz and maybe a little part is related to that while the bottom story is more abstract?
The matrix franchise was created by two transgender females, who call themselves The Wachowskis.
There is a possibility that it is a marketing campaign, but this assumption is based on pure speculation.
However due to the comments made by one the franchise's creator and her identity as transgender, one could assume that at least some part of the movie deals with transgender identity.
During the debut of "The Matrix" in 1999, the world was less tolerant of transgenders, so one might assume that the creators of "The Matrix" subtly incorporated the theme of transgender identity into the movie.
The movie may or may not be about the transgender identity, the interpretation is up to the viewer.