The closer dots you mention on the USA and MIM were the standard configuration on Fender necks up until about 1952. Fender then changed them to the further apart style you see on the MIJ. The kept this config until sometime in 1963, when they switched back to the former config. It stayed thus through the eighties at least, even with the MIA 57 Reissue, with Fender stating that they couldn't do the wider spacing with the equipment they had in house. The MIJ Fenders had the 52-63 spacing from the get go.
Fender now has the capacity to do either format, and have adjusted to the proper spacing on all the reissues (as far as I know), but other than reissues, I don't know if there's any rhyme or reason to which spacing they use on which model.
I don't know about the USA made Squire from 1991. Perhaps this was about the time that Fender was able to start making the wider spacing, and on some early models they got it too wide. It wouldn't be the first time they initially used incorrect dimensions for vintage appointments.
I have no idea why they made these changes. I've never heard any reason given.
2011 Gretsch G5120
2009 Agile AL-2000 Bird TSB
2006 Fender Classic 50's Stratocaster (My #1)
1998 Epiphone EJ-200