Read further, while the author didn’t realize what she was doing it is a trans narrative through and through, and the free dlc ending did contain the flag because by then she did know.
When Madeline looks in the mirror and sees her other self; when she attempts to abandon her reflection, who then drags her down the mountain; when the two reconcile and merge to become stronger and more complete… that was all unknowingly written from a trans perspective.
This feels painfully obvious to a lot of (mostly trans) people, and likewise it feels painfully obvious to me too, in retrospect. It has also become painfully obvious to me that I, myself, am trans. But these are things that I was not aware of during the development of Celeste, where I was writing Madeline and speaking from her perspective. Creating Celeste with my friends helped me reach the point where I could realize this truth about myself. During Celeste’s development, I did not know that Madeline or myself were trans. During the Farewell DLC’s development, I began to form a hunch. Post-development, I now know that we both are.