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Well there are plenty of online materials that you can read about the Japanese factory and the quality of their guitars.
Unfortunately the last couple of years, the Japanese Fenders are not sold in EU or US and it makes them more rare and precious for all of us. And the EU regulations have changed recently and some types of wood (which they categorise as exotic wood) is not allowed to be imported in EU.
Carlos Santana has a PRS with Brazilian rosewood fingerboard but he couldn't bring it to EU as this piece of wood is "exotic".
Anyway, all of the above have to do with each individual's taste. I have seen guitarists playing with a £199 Squier and you couldn't believe in your ears..
I know nothing about the Japanese models, but the Mexican and US factories are about 20 minutes down the road from each other, and use the same bodies from the same wood. Necks differ though. I think standard Mex necks are 50's style with one less fret and a different profile.
Exchange rate might affect the relative prices. The dollar is weak right now.
Incidentally, seeing as you plan to do your own thing with the electronics, I've got two Squier Jazzbasses, one early Korean model and one newer Indonesian (iirc) one, and in terms of body and neck, both are great. The later one had much better quality hardware as standard, but on the Korean one I ended up replacing pickups with Seymour Duncans, and the switches, electronics and control plate with genuine Fender parts. These are better quality than the Squier ones in either bass.