Nonetheless, I think you are being too generous towards Chinami and, to a lesser degree, Takahiro.
While, yes, she does seem to love Fumiya throughout the story, we can also see her desiring Takahiro since their first time and treating him lovingly ("please return quickly"). That softens the hypothetical dichotomy of her only physically cheating versus Fumiya emotionally cheating.
Fumiya was placed in an impossible position and while he is no saint, he also isn't a "villain" as you suggest and neither is Naruse. I would still say that the only "villain" is indeed Takahiro closely followed by Chinami. Takahiro didn't hesitated to jump on Chinami from day 1.
At the same time Fumiya and Naruse got progressively closer but never crossed the line. Controlling your actions is far easier than controlling your feelings and that's why, in my opinion, emotional infidelity will never and can never be worse than physical infidelity. Fumiya and Naruse only had sex years after the experiment while Chinami and Takahiro had it from day 1.
But when I frame Chinami has a 'villain" I don't mean she is "evil." She is just a mother and a wife whose husband has long stopped seeing her as a woman. While Fumiya is (was) loyal, the fact that he is unable to have sex with her due to a total lack of desire is something that has chipped at her self-esteem for years. Indeed the only "hentai logic" here is Chinami having sex with Takahiro to learn how to please Fumiya. If the manga wasn't cancelled, we would probably see Chinami resisting Takahiro up until the time Naa-kun was born and only after Fumiya lost again all desire for her she started the affair.
Of course, at this point we have to address the ED issue. It's ridiculous that mangakas need to frame ED as almost a supernatural condition against which nothing can be done. There are pills, there are toys, there are tongues and fingers. Fumiya might not love Chinami as a woman, but he loves her as a wife and a mother. If he at least cares about her, he could still have intimacy with her and pleasure her. But if that happened, it would be harder to justify both affairs as "ordained." And, of course, Chinami would look awful in the picture: "your husband is genuinely trying but you chose to betray him for an erect penis."
It's understandable that Chinami would start her affair with Takahiro specially after Fumiya lost all desire for her for the second time in their lives. She probably tells herself that the physical affair is just to fill the hole left by Fumiya because he has no desire.
And that is why seeing Fumiya and Naruse kissing passionately was a soul destroying moment. Also, probably it dawn on them that both their spouses were together during the event. When she sees Fumiya and Naruse kissing she confirms that the problem is not Fumiya lack of interest in sex. The problem is Fumiya lack of interest in her. She realizes that if she leaves Fumiya, she will mainly be hurting their son and herself, not him. He will be fine. Her womanhood, her life, her value as a woman is left in tatters. The only thing she has left apart from her son, is Takahiro's desire. If her marriage collapses, she will lose everything. And this also frames her saying to Takahiro "I almost died laughing" as the utmost sour grapes. It has to hurt knowing that if she didn't had the affair with Takahiro, Fumiya would likely never meet Naruse again. Probably until this point was "I'm seeing Takahiro so I can continue to be a good wife to Fumiya" to "I'm seeing Takahiro because otherwise I have nothing.' Oooof.
And Takahiro? Takahiro is just a penis with a good haircut. He probably cheated on Naruse before the experiment because he has no issues diving head first into Chinami. Ever since the experiment ended, Takahiro and Naruse went through a phase similar to the other couple, but I think that Naruse soon lost interest in him and used maternity to deny him sex and intimacy. Probably around this time Takahiro and Chinami resume their affair, but why would he wanted to move closer to Chinami if it was just an affair? He did so because in all likelihood Naruse made it clear that their life together was basically just co-parenting. It makes sense for a man with such a high libido and proud of his skills that his wife not sharing intimacy with him would be a severe blow to his ego.
So in the epilogue we see Naa-kun as basically as a copy of Fumiya. He dates Naruse's daughter and he likes her brother saying that "for some reason he thinks of him as a little brother." This is important, he feels that brotherly chemistry towards Akira but not towards Shii-chan. The hint here is not subtle. Also, when Naa-kun mentions she is jealous, she states, that she inherited that from her parents. I would say that Takahiro is the jealous one. But he can't say anything. If he ever confronts Naruse, she will leave him. So other than jealous tantrums he can't do anything about it. Confronting Naruse would also shed light in on his affair with Chinami and if everything was in the open, Chinami would try her best to saver her marriage so probably she would stop meeting Takahiro. Even if Fumiya left her, which is unlikely, Chinami would never forgive him for blowing up her family. And regardless of the outcome, Fumiya and Naruse would still be together. Naruse even changed jobs to be closer to Fumiya. This has to hurt
That is why Chinami and Takahiro go to each other's houses while Fumiya and Naruse always meet outside. Chinami and Takahiro only have sexual chemistry and their affair is not just fueled by lust but also resentment. But Fumiya and Naruse's affair is fueled by love. Not saying Naruse and Fumiya's is morally better, it's still an affair. But they have an affair because of what they mean to each other and not because of what they lack in their respective relationships. Fumiya stays in their marriage because he truly values his family and because of the guilt towards Chinami. Naruse stays in her marriage because Fumiya will never leave Chinami. Takahiro stays in his marriage because of his ego and because he knows Chinami will never leave Fumiya. And Chinami stays in her marriage because she truly loves Fumiya.
Also, Takahiro showing up at Chinami's during the day, in casual clothes is a telling sign that he probably doesn't have a successful career. Naruse probably pays the bills and supports them both. The only thing he has is sex with Chinami, in her home, in the entrance and in the bathroom. Maybe sometimes in the couple's bedroom if Fumiya is on a business trip. That's their "revenge." Poor revenge indeed since he is forced to raise Fumiya's child, see his daughter dating Fumiya's son and knowing his wife is with Fumiya in many of their business trips and overtime hours.
So to wrap up, Takahiro and Chinami got the short end of the stick, but they are laying in the bed they both made. The irony here is that if they had stayed away from each other and faced their spouses honestly, neither Fumiya or Naruse would ever meet again.