I think the answer is that Fender does not build Squiers themselves, they hire them to be built to a price by a contractor. They likely give them a basic blueprint, which could be in English dimensions, and then the contractor, be it Cort, Samick, or whoever, has to build the instruments to meet the print.
It's also possible that the contractor was given an instrument to use for measurements (thereby preventing the contractor from having exact dimensioning information that could be considered proprietary and sensitive) , and they had to arrive at dimensioning and tolerances themselves. That might be a better explanation for the variances.
I agree that it should be possible for perfect fit, but it has to be a priority on Fender's part, and I don't think it is. Squiers are intended to be less-expensive representations of Fender instruments, but not necessarily exact.
Roger