Uh no, it wasn't like that, this is a pretty big misinformation. Some indeed were like that but others were just like this girl.
And the same scene is on the anime. It's alredy on the timespan where they appear so just click on the video.
It is, I don't even know why some people in the west believes that this is something created from anime/manga when it's pretty much how it is in Japan for decades now. It's also true that many use underwear below it without anything outside of the skirt to protect, even if others do use some shorts below but that's more on something I asked my cousin so don't take it as a fact. I never lived in the country, but I was in Japan last year and it was my third time there since I have family on the country. Skirts, thighs and shorts are very common, even in winter (where obviously, most people uses some high tights to protect the legs of the cold). In Shinjuku and Harakuju you'll see that even more as young people are many times seems on there, even if many times you see older woman also using it. I saw many that looks like on their 30s using it as well.
Not even counting that japanese girls in school, for example, shorter their skirts not only to show some individuality but also because many dislikes how big the skirts are. In some schools of course the minimum size isn't bigger but some definitely are. My cousin which is a japanese teenager with 16 years (she was born there, her mother is brazilian and father is japanese) even said something similar about how she prefers it since she hates long skirts and it's why she uses some acessories to make it short, even if sometimes teachers and others from her school scold her but she does as her friends do the same and she thinks she looks better with it as well. Anyway, just something more personal as I was with and talked with her last year in person.
I'll post photos that I picked from google from japanese on street to give you examples.
And some for my examples of highschool/middle school girls with short skirts
There's much more examples out there with images that you can find on google from everyday people but I think I put many examples already. And of course, skirts aren't the only thing women and girls wear but it's one of the most popular in Japan for sure in women fashion.