You know, ignoring the shitstorm this thread quickly became, I kinda liked this comic. It was pretty bittersweet without being explicit in any way, neither in regards to the storytelling nor the actual sex scene. Sure there wasn't much description of a setting, but the narrative did a decent job of describing You's feelings and hinting at her background.
And yes, the story definitely portrays You as transgender rather than futanari. From what I've seen there usually isn't a reason why girls have penises in futanari hentai other than for sex, but in transgender works it's always portrayed more seriously and/or realistically.
I should probably state that this is all in my opinion and I don't mean to insult anyone who disagrees.