Who cares what Skye thinks or wants? The dev gave us a choice regarding Shauna because she is intended to be a main character and a main romance that a lot of players will pursue so a content choice is logical. Skye is definitely a side/minor character so if you don't intend to get into his pants, why do you care about what the character wants or identifies as? Does the simple existance of this character on a few scenes with text saying "him" affect your experience that badly? If so just skip ahead! I'm not interested in FtM trans content so I won't actively pursue him and that's it! Just another character in the plot, it's not like the dev will force you to have sex with Skye for a full update while he's screaming "I'm a dude! I'm a dude!" on a loop.
Honestly I appreciate the dev for having the balls to include content that's not too popular or even seen around here, even if I'm not interested in it. It doesn't ruin the game for me because it's optional and I don't get upset by reading "him" while looking at someone with tits and a vag. Live and let be.