The train chapter shows more about her independence and decision to follow her own path than it does her feelings for Fuutarou.
Beyond that, there are any one of a number of points where Itsuki could have stepped in to demonstrate her changing feelings at times when it would have been crucial to developing the plot. The first quint whose feelings for him he takes specific note of in any way? Nino and her "ill will" at the end of vol 1. The towel scene that followed could have easily switched Itsuki and Nino as well, with only minor tweaks needed to the story in that chapter..
She could have been the one for whom Fuuts gathered the others at the rooftop for the fireworks. She valued her memories with her mother enough for that. Instead, it was Nino, and it was also Nino who begrudgingly thanked him at the end.
She could have found the wherewithal to deceive their Dad about their midterm results. Yes, she values honesty, but it could also demonstrate the growing strength of her appreciation of Fuutarou that she was willing to lie/deceive for him.
He could gave saved any of the quints (except maybe the athletic Yotsuba) when they jumped in after him, but it was Nino, a moment which was critical in her developing feelings for him.
Given how Itsuki had met with Papa in ch 54, she could have relayed the results to him in ch 59, instead Nino did...and we got a confession out of it.
And so on.
Itsuki's development has stayed steady at the friend level for a long time now. It's a little late in the story to suddenly say she's going to start developing feelings for him after giving little indication there's anything more there since at least the end of Seven Goodbyes. It's poor character development and poor structuring of the story.
Maybe that's Negi's problem in the end, but he seems smart enough to avoid that. One hopes his editor is as well. I think she's a decoy or feint. He's using the power of first girl status to district us from the real story.