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Hi. I completely agree with you. This applies for all guitars simply because not every piece of wood is identical with each other, even if it comes from the same tree.
I have played with Squier Strat - Protone series and for my hands and taste they were more enjoyable than the Mexican ones. This doesn't make the Mexican ones worse guitars.
However, the japanese factory has quite a reputation that's why I would be interesting to try them first.
My main goal is to get a quality guitar, without taking into consideration the pickups or the electronics. I want to make a Frankestrat but I want the base (body and neck) to be as good as possible for my budget.
It's my experience of Fenders that supposedly identical models can feel and play completely differently. I've played tons of strats and the only two I ever liked were my mate's 80's US one and the 90s Mexican one I bought off a forumenger.
Therefore, don't restrict yourself to a certain era or country of origin - play as many as you can and buy the one you like the most.