I agree with your analysis and your points were exactly how I treated/read this series. It was realistic as it could be and I treated it the same way. But I guess to me I'd still call it a "happy ending". In reality, there is no such thing but in this surreal universe sensei created, just the idea (and hope) that the cycle of pedophilia is finally over is giving me the "happy ending" vibes. I read the chapter so many times but I really don't feel Harada hinting that the characters' futures are going to dark, back to child rape or anything related to it.
Yui, well aware of his situation and definitely understands everything better than Kei did, still chose Kei and with Kei taking responsibility and not getting abandoned, I don't see him becoming this universe's next pedophile.
Kei, finally accepted an answer to the questions he had since he was separated with Ojisan.
Ojisan, yes I know his new child's a BOY, but his face, finally shown, is totally empty, rather his head is. Like he has gone some serious psychotherapy to correct his mind and now living like a normal person, stripped off of his memories and his deeds.
Nii-chan was a real clash of reality and fiction. I feel like sensei turned a study on pedophilia into a story wherein more people can understand pedophilia than reading a scientific article or book. Harada is really one of a kind.
This is not a happy ending. This is not an ending that condones or romanticises pedophilia. This is a ending that bluntly shows what happens when pedophilic influence is exerted on a young child with an impressionable, breakable mind.
Despite the seemingly 'happily ever after' ending, the overarching atmosphere of bleakness clearly suggests otherwise.
Yui becomes a true victim of pedophilia, someone who obviously knows how horrendous the act of it is, and yet chooses to believe in his relationship with Kei, chooses to believe in misplaced love. Kei becomes someone who finds himself in a deadlock, he can't assimilate back into society after what he's done, he knows his own mind and concept of love is far too corrupted, far too twisted to ever find love in the boundaries of 'conventional' love—and so, realising he's too weak to break free from the cycle, he chooses to end it by settling with Yui. His last and final victim, and his only solace in receiving affection.
Harada shows how there are pedophiles out there, who continues to live on a life free of repercussions, no matter how despicably, how damnably they relished in the pleasures of acting on their pedophilia. Or on the flip side, they are trying to show how there are pedophiles who reform themselves, who try to pick up the pieces and create a semblance of a 'happy' life they can never have if they continued engaging in such a deplorable behaviour.
Harada shows the ugliness of child rape, and the vicious cycle of it where perpetrator births a victim, which in turn, is likely to develop into another perpetrator (just look at the statistics of the sheer amount of child rape victims who become child rapists themselves later on in life). Or perhaps, they remain victims, their mind and body forever bearing the invisible scars of a memory that they can never forget, or even worse, their minds become so irreparably broken that they feel it's alright to give an adult free reign of their body.
The story even shows how uncompromising and narrow-minded society is in their treatment towards pedophiles. Like homosexuality, it's not something that can be treated with things like conversion camps and sex therapy—some experts even argue that it can be considered a sexuality in and of itself. And yet, people still endorse these practices. It's not the right approach and it'll not only make their mental condition worsen, it may even sow seeds of discord and discontent inside them and their unhappiness towards society may cause them to eventually lash out by falling into pedophilia.
What majority of the society doesn't comprehend is that a person can have pedophilic tendencies, and yet have the moral courage and restraint to NOT act on it. The sad reality is that most people immediately jump on anyone who is suspected to be a pedophile, even those who may just want to seek help in controlling and understanding themselves. In society's eyes, they are branded irredeemable and contemptible creatures who are better off dead—people don't see (and don't try to) the difference between a child rapist and a pedophile, it's a blanket assumption that does much more harm than good. And I think, that needs to change.
I think it's wonderful that Harada manages to bring up all these points of contention through a mere 6-chaptered manga, and I believe this attests to the skill and talent they have in crafting not just the twisted stories they are known for, but also executing stories that are morally challenging and emotionally nuanced. To call this a happy ending would be doing a great disservice to the masterful narrative and the sheer amount of work poured into creating such realistic characters, full of flaws, and yet they shine with their raw humanity.
(This is not as coherent as I wanted it to be, certain words elude me and there are probably lots of grammatical errors since it's already been 2 days since I last slept... but how can I sleep when I see an update from Harada amirite?)