"Moreover, Raene wanted to be a girl so it doesn't even make sense that she kept her cock which she didn't want to have to begin with, I genuinely was surprised the first time I romanced her and discovered her cock even though she totally wanted to be a girl as in not keeping anything from her male past life which she never wanted to begin with"
^^^^^^^^^^^ 100% this. I legitimately assumed that the protagonist would have almost immediately assisted in helping Raene complete her transition to full girl instead of actively taking advantage of her male genitals. Especially in a far-off future where no doubt such a surgery would be very fast, easy, streamlined given how futuristic everything else is, and she's from a very wealthy family. It could have easily been a side event as part of romancing Raene, and I guess it would be skipped if you don't romance Raene. But you are right, that would be asking way too much from this developer.