@1986ctcel You're right, I am ignorant of the specifics of the story because I have not read it, this is true. However, I'm not arguing the specifics of the story. I am simply analyzing the reactions of the characters that you guys have revealed to me on a psychological level. And nothing that you have said to me has subverted what I've said whatsoever. The MC admits that he is attracted and likes this Yuki, from what you've said. The question is, would he harbor the same feelings if Yuki wasn't a cross-dresser? Considering how uncomfortable and weird he finds the idea of his attraction to Yuki because of the fact that Yuki is male despite his feminine appearance and bearing (I'm assuming on the attitude portion, since the MC mistook Yuki for a girl from the start, so I figure he must have feminine personality traits), I highly doubt it. The entire hook of the series from my point of view, just from what you have explained to me here, is that a straight male is confusedly attracted to his cross-dressing male friend but in the end decides that his sexual preference still lies with girls. Again, I posit that if Yuki had never cross-dressed, this entire pseudo-romance between them would never have happened. The MC is clearly only sexually attracted to Yuki because of his feminine appearance, and all of his interactions with him will be influenced by that appearance. That is what I meant by deception. I mean, does Yuki want to become a fully-converted girl (as in getting the proper operations and treatment)? If not, then the idea that the MC is only attracted to Yuki because he looks like a girl will most likely end up blowing up in his face the instant they get to a physical relationship and the MC remembers that Yuki has a penis. I'm not trying to say the way the MC's decision was made is good, but you're not willing to admit that (just from what you've told me) all the signs were there that this would never end up with Yuki and the MC being a couple.
Also, as far as "Saying that just because the MC wouldn't be interested in Yuki if he didn't crossdress and look so girlish is like saying he wouldn't be interested if a girl didn't have nice curves or a good complexion or if she was obese.", I think you are vastly underestimating the influence that a person's physical appearance has on the interactions others have with them. Humans are honestly very shallow creatures, and physical attraction is a very important first step to any romantic relationship. So, yes. I am saying that the MC more than likely would never have fallen for Yuki at all if he had never cross-dressed, and also most likely wouldn't be attracted to a girl with the traits you have listed.
Lastly, a friend of mine brought up a good point that I forgot to mention. A male can find another male attractive without wanting to be with them sexually, which let's be honest here, is the basis of any healthy romantic relationship. I find men attractive all the time, I recognize them as an attractive man, but I don't want to have sex or anything with them. Considering the MC's discomfort with the thought of being attracted to Yuki when Yuki is the same gender tells me that the MC doesn't find Yuki attractive the way a straight man finds another man attractive, but the fact that Yuki looks and I suppose? acts like a female.