I see how you jumped to that conclusion, but I think you're conflating two things. First, back then it was sadly very common for children to be considered sexuality mature (age of consent in some European countries is still 13). That's been largely resolved by legal frameworks today (paedophiles still exists, but everyone agrees what they're doing is bad)

And the other idea you're conflating is that (which I think the article dispels) is that feudal Japan consider youth to be tied to age. For all we know, it might be a concept unfamiliar to us westerners that got projected onto "youth" to make the article approachable to Western audiences.