I get the confusion. Tomo is boggled by gender to a degree vastly more common for a dense queer teen, so this chapter is the yaoiest of all. I haven't been taking comments about thinly-veiled yaoi all that serious until now, since Ibuki's hidden personality traits are very feminine coded and more common in women. Even so, the only definitively gendered part of the friendship is how other people treat Ibuki, which doesn't tell us how Tomo comprehends feminine girls and femininity in general.
I wish the story had been clearer about this earlier. It wouldn't have even been that hard, just show him interacting with girls in class slightly more or say more about how having lots of sisters shaped him. Or something. Anything. Without that prep or foreshadowing, this chapter as written would've worked better if the story was gay. For an important moment of making the emotions relatable for readers who don't read queer content, which is a big strength of this story and other platonic-ish childhood friend stories, this chapter fumbled imo
Just realized: It's about the same issue as when the author didn't explain the pair only became friends in highschool, until an extra.