Sena's casualness about confessing was a bit of a surprise. She's been very embarrassed about that sort of thing before, blushing and turning away. Not as paralyzed as Yozora is (shaking in fear just from having witnessed that), but definitely not as clear and casually assertive as she was here.
I do wish that Rika was less meek about her own feelings. I kinda figure she thinks that Kodaka likes Yozora and Sena the most, but Rika definitely would have had a clear advantage had she confessed first. She is his self-admitted type, after all. She even would have done it in a way that Kodaka definitely wouldn't be able to lie about hearing it, since she's well aware of his habit.
You're right to a degree, but Yuki's assertions have some evidence to back them up way back in the first season and first and last episodes.
Kodaka's never had any friends, ever, other than Yozora for a month or two at most. His father moved around constantly for work, so they were never in one place for long, and Kodaka's appearance got him ostracized (often physically attacked) wherever he went, getting worse as he got older. Kobato really lucked out by looking more like her mother, as we know now, she's super popular. But she shares that shyness and is only close to Kodaka also because of the constant moves. Again, lucky for her, that shyness only makes her more popular with her classmates, even if she doesn't want it. Kodaka got an even split of the genes, and looks threatening all the time.
So now that Kodaka has finally got friends, he really does enjoy the status quo, and wants to keep it. He knows as well as Rika that they're already all friends, even if Sena and Yozora wouldn't want to admit it. But Kodaka also probably recognizes that both Sena and Yozora really like him. He knows that if he picks someone other than Yozora, that he'll at the very least lose Yozora again. Losing his only friend in a way where he was simply abandoned probably traumatized him deeper than he was willing to admit, the same way that Yozora's fear during that incident got worse and worse, giving her the crippling social anxiety disorder she has today. It also doesn't help that he waited and waited to tell her he was moving away, and when he finally did, it bit him in the ass because she hid around the corner from him, too embarrassed to show him that she was a girl. That decision to finally say something resulting in never seeing his best friend again doubled the effect the event had on him. It doesn't really help that he didn't notice that Sora and Yozora are the same person (but really, who would?), she was too afraid to make up for lost time, instead scheming her way to being near him, and when he finally realized it, she basically told him that the past is the past and they only were friends, they aren't now.
Now he prefers that nothing be said, the closer people get, the harder it is for him to part.
Kodaka escapes situations where he feels he is getting too close to others as a method to avoid the pain he felt when he lost his only friend. He'd rather drift apart slowly than experience that emotionally shocking kind of split again.
tl;dr: Sena surprisingly casual and forward, I wish Rika was less meek, Kodaka likes status quo, but was deeply traumatized by Yozora abandoning him, the issue compounded by her severe social anxiety a decade later.