I got mine from the Shibuya Apple Store but it's locked to docomo. They do sell "SIM Free" phones but since they're unsubsidized, they're significantly more expensive. That said, all iPhones sold in Japan, starting with the 6s/6s Plus, can now be unlocked after six months by simply telling the carrier you want it unlocked. They all charge a fee for this (3000円) but at least it can be done, finally!
I believe they'll have different model numbers. Sometimes making it hard for replacements in different countriesI heard opposite answers. Anybody bought the phone from Apple Store in Japan?
I bought the 6s plus on launch day at the Ginza store, SIM unlocked, and then signed up with an MVNO. The phone model is A1687. You can google the various models to confirm country band coverage.
Regarding an MVNO, I recommend the BIC Camera SIM which is provided by a company called IIJ. Data plans are cheap and coverage is good. It uses Docomo's network. You will need to sign up for a 1 year contract and pay a termination fee if you leave early but it wasn't outrageous from what I remember.
Regarding the big carriers, yes they subsidize the phone price but charge a lot more for their monthly data plan. If you do the math, it's quite a bit cheaper over 2 years to go the route I did.
Hope that helps.
iPhones include a lot of bands. You just need to know the model available in Japan and then google the bands used in each country to look for a match. For example: http://www.apple.com/iphone/LTE/