Ohh, thank you for taking the time to respond! I'll keep my reply brief as I don't think there's too much to add. (Putting it below some spoiler tags as I will be delving into some discussions of abuse.)
===SPOILERS===
I think most of it can just be boiled down to the fact that I intended the story to indeed, be highly allegorical. Hence why the Doctor is defined by his hatred towards the world, and he has obsessed himself with creating a "perfect woman" who will solve his problems. It's why I don't give him a name, or even a face - he's not a person, just like how he does not treat Yumeko like a person. It's also why I wrote the story in second person - it is not "Yumeko," not "I," but "you" - the player.
Overall I wanted to be able to portray the experience of being in an abusive relationship or under oppressive gender expectations without necessarily conveying it with physical abuse, or sexual assault - since I think that media tends to gravitate towards portraying the suffering of women in such a manner: in a very physical, "in your face" way that is easily understandable, even if you've never experienced such a thing, while ignoring the more subtle ways in which women can be broken down, emotionally and psychologically. My usage of an AI here was mainly meant to convey her utter lack of control and experience, and how the Doctor claims ownership over her - as god and creator.
Admittedly I wouldn't make a commentary on AI in general, or the ethics of abusing an AI; I think you have a good point, and I think there would have to be discussions about "what constitutes a person" that I am nowhere near well-researched enough to have LOL (and I do think such concepts have already been explored by people much smarter than myself). I actually think that, in the Statue ending, in which she is still simply an "AI" - a set of coded instructions - her fate is quite kind, as she cannot feel pain.
Overall I did intend for Yumeko to be human, or to be interpreted as such! But of course I don't intend to prescribe a specific way of interpreting the story. I think expressing sympathy for the Doctor is quite kind, and a valuable way of interpreting the story as well.
Thank you again for the thoughtful comments, I quite enjoyed reading them!