Yes, I think if there is an issue you just send the camera back to the retailer who then negotiates with the manufacturer. Major japanese shops are usually very very reliable people - Warranty service via the retailer used to be the case everywhere in fact. maybe B&H and co don't offer this degree of service anymore in their effort to lower costs.
I think there are no federal customs tariffs on still cameras - you can call customs and ask.
I bought my 645D in Japan in 2011. The price difference was several thousand dollars, even including customs. I bought it through Mapcamera in Tokyo. Pentax Japan didn't offer an international warranty for it's cameras during that time and I am pretty sure that it will be the same with the new 645z. After 12 months I had a sensor problem with my camera and luckily they exchanged the camera for me, even it was not covered by the warranty.
I also bought several lenses from Japan through ebay and also through Yahoo auctions. Two times I got a lens with fungus inside, even they guaranteed that the lens would be in perfect condition. Due to the humid climate in Japan, I would advise not to buy old Pentax glas from there. There is a seller in Shinjuku who sells a lot of used Pentax glas on ebay. He writes that the lenses are checked by the official Pentax store before he sends them to you. But still he sent me a lens with fungus inside. On the pictures you can see a female model showing the lens. Avoid this guy.
So if you want to be 100% sure that you get a new body, I would buy it directly in Japan or let it send you through a website like whiterabbit.