The stories you write come from somewhere within you. Your keyboard is not automated, and your hands do not have lives of their own. When you mentally compose a scene before committing it to the written word, what is it exactly that goes through your mind?
The assumption that the judgemental reader you describe holds, at least in cases of kinks they dislike, is that the writer must have certainly been imagining something they want to actually happen. They are simply codifying their genuine desires. Often the assumption includes that they picture themselves in the position of one of the characters - especially the more offensive one, if they exist - or otherwise are taking an action or finding themselves in a situation that they cannot easily bring about in reality.
Of course, the human mind is not so superficial, and stories are rarely so blunt a translation of an author's thoughts. Consider the textbook example of incest. The judgemental reader would, essentially, assume the worst of the writer: that they genuinely want to have sex with a family member, that the only thing stopping them is an issue of either legality, social acceptance, or reciprocation, and that the story is merely a manifestation of this actual unrealised desire. If you are not literally writing about a family member, then the differing characters and context must, according to this reader, be only a thin veil.
Truthfully, there is a multitude of layers of possible reasons behind a writer choosing to compose such a scene, and they each lie on a spectrum wherein the literal desire for personal incest occupies just one extreme. Perhaps the writer does not personally wish to participate in incest, but would still like to see it really happen, between their own family members or perhaps related friends. Perhaps the writer merely enjoys the idea of incest and knows they do not actually enjoy it in reality, or at least has the self-awareness to realise as much. Perhaps the writer does not specifically like incest but more generally taboo sex, and incest is a prime example of a taboo because it remains a very real one in most modern societies - in fact, writing erotically about incest is often its own sexual taboo, and thus the author is, in a way, participating in a fetish, just not the particular fetish of incest. Perhaps the scene is merely a natural addition to the plot, and the writer is not actively opposed to its inclusion; perhaps the plot leads so explicitly to that place that the author finds themselves with little choice but to write it, even if it is not their preference.
Each of these reasons is less literally related to incest than the previous, but none of them are unreasonable motivation for writing an incestuous scene. In fact, if the final product has sufficiently deviated from the obvious case of writing about an actual personal fantasy, some of the most unacceptable and even disgusting sexual acts may be worked into a creative piece while barely affecting its reception. A Song of Ice and Fire is a mainstream piece of media with sex scenes involving rape and minors, off the top of my head, and in the series adaptation Game of Thrones there is probably more on-screen rape than is really warranted by the story, but the books have no moral controversy among the general populace to my knowledge, and the worst thing you ever hear about the show is how disappointing its finale was. Even personally, the most infamous aspect of George R R Martin's reputation is how slow his writing process is, of all things.
There are shades of grey in the issue, but some of them are very light and some are very dark. Some people have more black-and-white thinking, and some only ever see just one shade. Your genuine perspective on your subject matter might not always come through in your writing, but then sometimes it is abundantly clear. It may be overt in very serious works that the author was not masturbating when they wrote about the abuse the protagonist suffers at the hands of the irredeemable villain, and in something called "I Kidnap And Rape My High School Bully" it may be overt that the author would jump at the opportunity to drug the real Cindy Brown and handcuff her to his bed, but most CHYOA stories, being pornographic but not personal, lie somewhere in between.
