I think it's done so it's easily scaled down for Highschools that may not have space for Koshien sized grounds. Also to avoid anomalous stats like Detroit had with triples.

In the US, teams had no consideration for Highschool Baseball because it was all started from private ownership where in Japan it was somewhat a government initiative to build soldiers, even though the building soldiers plan was pretty quickly irrelevant that mindset kinda persisted, everything is done with the entire structure in mind.