Maturity means also to be able to discern between fiction and reality: a problematic story or topic is not a declaration of absolute truth. Sometimes authors decode to be controversial just for the sake of telling a different story.
The trick is here: appreciate it without taking it as a truth.
I think it's more or less the same mechanism we put on when appreciating abstract/conceptual art: the artist sticks a banana to the wall, but we can see the message beyond that and still appreciate it, without believing that a banana is a great piece of art.
That is true! And I really like the analogy you used.
I feel as if is part of growing up to analyze media as a device to project reality and to expect it to reflect absolute good by whatever metrics you were told were right by the community around you, only to later realize that if that were to be the case, many of the great stories that exist simply wouldn't anymore. Because art doesn't have to be "good" to exist and to connect with people.

I had kind of the opposite experience when it comes to this manga. I remember being so uptight and nervous when reading this when I was young, really hating the teacherxstudent trope, and the way Kousuke treated poor cute Masahiro. Although nowadays I still think Masahiro is still too precious for this cruel world, I actually find myself enjoying this a lot.
In a way, it's part of growing up, and unlearning shame. I don't think it's perfect, but it's very fun and charming, the dynamics are cute and play into the fantasy way less dark than what it could be in a good way.
And for the comments that once reflected my own experience as a young queer boy, who always felt as if he had to be this holy beacon of morality lest I become a monster for the fiction I consumed: while I can't stop anyone as a complete stranger on the internet, if you're not mentally ready to read this, I suggest you skip it, and don't engage for you own peace of mind. I suggest you find fiction you enjoy, and hope that you're able to enjoy it to its fullest and free of shame. ヽ( ̄▽ ̄)ノ