Great points, really enjoyed reading everyone's response, but I'd like to add some clarifications(imo ofc).

Reiji turned Chako down sexually only once. They only had 2 chances to have sex; at the manga Cafe and when he visited her at her home after her weight loss. At the manga cafe,, Reiji told her that she was special to him, and that by having sex, she would be like everyone else. This same event actually happens in the author's previous work, Himegoto. Reiji was willing to commit to have sex with her(like Nagi, he is a person who will try to satisfy others, even if he is against it) but she declined, since she didn't want to lose that special place in his heart. I think this is important to remember, since she is the only character he has had a positive appreciative comment for.

Gen never really "loved" Reiji. Reiji himself conjectured this, but given the events its clear that who Gen actually loves is Yuko. Gen himself probably twisted his perspective of loving Reiji as a coping mechanism, making himself believe it was for Reiji when it was actually for Yuko.

I don't think Chako "tricked" herself to like Reiji. I feel that Chako has loved Reiji, ever since before she realized it. Yes, at 1st, she did see him as someone pitiful, and indulged in this "superiority", but after the first kiss playground event, she saw him in a different light. Maybe even before then. It's not like he only said some honeyed words(which he did), but it was also all the previous interactions that he was something important to her. Leaving Tokyo was just a pretext; she could have done so during the Reiji-Yuko standoff if she asked for Esemori's help, but what she really wanted was to be with Reiji. That's why she was so dejected when he abandoned her.

I also feel that you may be undermining Reiji's concern for Chako. I still believe that she holds a special place in his heart. Right now, I think that what Chako is going through is very much like what Reiji has been through and that the penultimate climax will be how he pulls her from this depressed state. You compared Chako to past-Saki, and for good reason. However I think that she is more like past-Yuko where she is slowly being pushed into a corner(not considering possible past-Yuko machinations) and needs(wants) to be saved.

This current interaction with Nagi is just a means to that end.