“just because a man and a girl are together does not mean that they are dating” - sometimes even the most experienced and professional shipping goggles miss the mark.
From what I understand, this chapter saved Kobayashi's stupidity because it confirms that she said that to Senpai as a lie to keep him away, but this chapter tells us that she is open to accepting this relationship and even slightly suspicious because she realizes that they disappeared.
So Chii didn't figure it out, but all those looks in the previous chapters makes it clear that she's noticed the kind of guy she is and thinks it would be great if they dated, which is sweet. Final sequence was quite pretty.
We're due for one more arc this volume (4-5 chapters) and Norio usually writes the volume to have a big ending so we're due for one more big development.
With the reminder of how close she is to Kobayashi, to the point her own boyfriend is jealous, and the, once again, failure to tell her about their relationship; it feels like we're setting up for some real drama when she eventually learns it.