Always interested to understand why things are where they are (e.g. proximity to Korea/China, sheer expense of Tokyo or somewhere like Osaka for a large industrial operation).
Tokyo and Osaka houses headquarters, manufacturing is almost always in some small town. A big benefit is Japan has a flat consistent tax system. Towns and prefectures cannot compete with tax policy or tax cuts. Thus factories are much more diffuse. The large corporations can bring their support networks with them but when recruiting high school graduates a big plus is to be local. Thus a town might have a couple large factories which can consume the high school graduate supply.
Occasionally you'll see various R&D centers. Those tend to be within an hour or two from the major metro. Far enough away the companies can build large campuses and employees can buy large houses for their family.
For example HAL Labs, the company which makes Kirby games, has an office in Yamanashi. Which made them one of the rare non publisher video game devs who do not rent.