Baby X
In many ways, X themself is a metaphor for gender nonconformity. While parents of gender nonconforming children would likely not refer to them as an X, the replacement of "boy" or "girl" with a simple letter underscores the extent to which X does not subscribe to a gender binary.
Clothing
In the story, clothing is a metaphor for the commercialization of gender and the gender binary. When the Joneses go to the store to purchase clothes for X, they have to choose between either pink clothing for girls or blue clothing for boys. This moment suggests that society's perceptions about gender are influenced by marketing and capitalistic interests.
The Light in the Room
When X is examined by the psychiatrist, there is a light that can be observed coming from the room. The Joneses and the Other Children all perceive the light as a different color, but the other parents do not see the light at all. The light becomes a metaphor for tolerance and open-mindedness, which the parents at the school lack.