Yep, a prefecture is basically a region really. I have been to the GT86/BRZ Subaru factory in Maebashi, Gunma Prefecture for a tour back in 2014.
My GR Yaris is a Toyota only affair which is a very good thing in my mind, built in Motomachi Factory, Toyota City. What is interesting is that there is a lot of hand assembly with the GR Yaris apparently taking 10 days to complete compared with around 15 hours start to finish including testing etcetera for a regular car. Some engine parts being hand finished as well as the Takumi (Japanese for master) technician who puts their name to it. The forged carbon roof is hand fitted and the 200 extra weld points are done by hand for extra chassis stiffening.
This vid is an interesting watch showing much CEO 'Morizo' has been involved with the car: