Really? I've never encountered that when ordering from Amazon JP, same Japan editions as every other Japan website.
Non-Japanese versions are marked as import & generally more expensive.
My Sgt. Pepper set had SHM-CDs. I believe the Imagine box does as well.
The Japanese editions of these sets almost always have superior packaging etc., than Euro or domestic versions, that's why I buy them and pay a modest premium.
One exception was The Beatles 2009 Mono Masters where all of the sets were produced in Japan