As the infamous Ed Wood would say, "Haven't you heard of the 'suspension of disbelief?'"

I guess I'm okay with everything looking European-y with Japanese actors. Heck, American films about Japan hire half the cast with Chinese actors and actresses anyway (the leading actress in Memoirs of a Geisha is
so obviously Chinese and definitely
not that it ruined it for me).
They could film some of the film in Nagasaki. There are a lot of European buildings in the Dutch Slopes there.
Some staunch critics of Japanese society like Alex Kerr have fits about Japan losing its traditional aesthetics. There are a ton of new houses being built in my immediate area, and not a single one of them resemble a traditional Japanese style with the sloping eaves, tiled roofs, and shoji screens. I do, however, see plenty of bay windows and such. These homes look more akin to Western-style homes.