Kudan appearing at the end of Koto's route is rather horrifying once you get to the True Route. Sawako isn't caught on any route except the True Route, and she's been targeting Touko in order to get her hand. While Sakuya's presence would certainly dissuade her on Touko's route, she'd have no such protection on her own and no reason to distrust her loyal servant. While you'd probably think Sakuya's line "What happened with Touko-san remained as an old scar, like a scab that could be torn off with the slightest knock," during Koto's ending is a reference to them drifting apart after Sakuya chose Koto, that line combined with the reveals in the True Route leave Touko's fate much more ambiguous.
