Level3, Verizon, and Cogent have been well documented to be points of failure on the internet lately. (Use
http://www.internetpulse.net/ during prime time to see how bad it gets lately) It's probably that by connecting to Japan's data centers you are entirely bypassing those nodes. So it makes sense that you potentially would see the problem going away by changing data centers based entirely on where you live in the country.
Also, you must consider that some ISP and backbone providers throttle certain kinds of data and FFXIV seems to fall prey to that.
It's these two things that make programs like WTFast so effective. You can route around the bad nodes, and it masks your data so it doesn't appear to be a video game therefore bypassing the packet sniffer's attempts to throttle.
TLDR: It's a more complex issue than "I have lag so the servers suck." Google around a bit and you'll see other games are having this problem too.
No it doesn't. It's a physically distinct location. One can go down without effecting the other for various different reasons. It doesn't begin to explain anything.