Just because the protagonist happens to be a Junior instead of a senior doesn't make the age gap worse. They are still three years apart
I don't mind the age gap, nor have I really thought about what possible ages they could be, but that's false actually.
If you just state "a 3 years age gap isn't that bad", well, it'd be true, in general. When people are in the thirties, or even twenties, 3 years isn't a big deal. When you're in your teens however, 3 years is way more significant. If a 14 yo girl had a 17 yo boyfriend, most of her friends would probs be like "ehh he's kinda too old, isn't he?"
Idk about you, but if Towada's starting middle school, wouldn't she be turning 13? I know for a fact that when I was in 6th grade, ppl were turning 12. So, Haru would be turning 16, probably. Unless the Japanese starting their school year in April changes anything, but that I wouldn't know.
A 13 and 16 yo dating isn't flagrant or anything, but generally, some people will express concern over it (as well as there will be those who don't think it's a big deal at all)