Hello my friend, thanks for the questions and the comments! I appreciate your thoughts and I don't think you come across as negative or anything, your points are very thought-provoking and are good topics for the IF community.
The way I see things as I write at least is that beautiful doesn't just apply to women. I find some women handsome and others beautiful and the same goes for men. (*Also inferring that you're referencing the scene where MC has a little breakdown after their bath) *I know men (cis) that are quite bashful about their chests - but it can also be fore the marking - that whole scene is just a general point of weakness and vulnerability for the MC (and the MC is also completely nude from top to tail, save for the towel around their shoulders/back). I wanted to error on the bashful side of things.
I've debated about adding a few more choices in the first couple chapters to give readers a heavier hand in the MC's development, and in the future chapters I am trying to add as much variation as I can account for according to the variable values set by previous choices. It gets sticky for sure, but I'm hoping to get better at shaping as much as an individual experience as possible.
I appreciate that you're finding things to be mostly a-gendered (I use she/her, but I identify more ambiguously and often more masculine though the lens I was raised with was feminine). When I read IFs, I primarily have MCs that are men, but I also will play through as women too (just not as often), so I want to try to focus more on the personality/characteristic of the MC and not necessarily ascribe masculine or feminine to their choices. I honestly don't always notice gender-inflection while writing my IF, but I know it's probably there (and I'm oblivious sometimes >_<). The issue is that my interpretation of those things will differ, as you can already see. But, like all of us, it's a work in progress and I hope to refine it as much as I can for such a wide audience.
Your input is very much appreciated, and you've given me some things to think on as I work! ^_^ (Sorry for long reply, and I'm thrilled that you like the dads!)