I agree that it's very clear Subaru isn't trans, but in my opinion this does not detract from the story in any capacity. I think there's undeniable value in exploring different types of relationships with gender and gender expression, especially when they fall outside of the explicit binary of "I'm a man / I'm a woman".
Of course, there are also some amazing trans-focused manga out there that blow it out of the park, but I'm still very fond of the niche Kasane to Subaru fills, personally. "Otoko wo Yamete Mita ~Gan ni Natta no de Josou shite Koi wo suru Koto ni Narimashita~" is a manga that doesn't have many chapters so far, but it's shaping into a really compelling trans narrative if you're interested!
(also my crops have been HELLA watered by this chapter
tysm for the tl)