The leading theory for what causes people to be trans (or gay for that matter) is hormonal fluctuations at critical points of fetal development. So we are born this way.

The evidence for this is really poor, the entire field of the hormonal theory of sexuality (and gender) is garbage

There’s lots of good literature on transmedicalism

Anyway someone who subscribed to that theory would say that a micropenis would be consistent with low fetal testerone and this story would be readily believable by them - far more than a trans woman who was born with a macropenis.