Board Thread:Questions and Answers/@comment-24.99.111.181-20150102193131/@comment-35248429-20181213080215

In the SEED games the Amusphere automatically represents your gender dependant on your brainwaves. So you can be biologically male and still get a female avatar if the amusphere reads you as such.

While it's not confirmed 100%, that he got the avatar from playing time is what is suggested by the players themselves and never contradicted.