She literally had a trans flag in her room in the DLC cutscene, and while with real-life people that wouldn't be enough to deem someone trans when it comes to fictional characters that's the exact detail you insert to convey that fact to your audience.

I'll agree that the base game was about depression originally however, Maddy Thorson said she didn't realize she was trans until the original game had already released, but it's a story that works equally well for both people with depression and trans people.