Good, it's unrequited yuri instead of pedophilia.
I didn't know Yuuto was a per-pubecent boy. Checking...oh, he's in high school, between 15 and 17. So no, Natsumi isn't some pedophile for flirting with Yuuto.
Anyway, I do find amusement in the "Natsumi MUST be lesbian 'cause we are going to ignore all of the shouta stuff she's done!" If anything, Natsumi is bisexual. If you look at the non-canon stuff on Shiromanta-sensei's Fanbox page, you'll see the author does ecchi stuff between Natsumi and Yuuto as well as Natsumi and Futaba. So Sensei sees Natsumi as bisexual, otherwise why draw Natsumi x Yuuto stuff?
To me, there's no doubt that Natsumi has a thing for Yuuto. She doesn't push it hard because he isn't of legal age yet. I suspect in some ways, he reminds her of Futaba. She enjoys teasing him and she clearly knows his feelings for her. But she doesn't push him away, and I don't expect her to in the future. At best, she might do the traditional, "wait until you are legal, and see if you still feel the same way about me then" trope.
As to the chapter being canon, it was part of volume 9. Apparently, Shiromanta-sensei wanted to explore the notion of falling in love with a friend, and the fear of changing the relationship with said friend because of romantic feelings. In Natsumi's case, she chose to keep Futaba as a friend rather than push her away with unrequited feelings.