The article is greatly exaggerating the potential scope of this. The underlying case involved reselling books that were imported without authorization of the copyright holder. When you buy an iPhone, it was NOT imported without authorization of the copyright holder. That's a huge difference.
Once you buy something, why would you need the original seller's permission to import it? I find myself personally concerned: I am studying Japanese and there is a paucity of media (books, video, et al) available in Japanese in my country. What might seem reasonable, such as arranging for books to be shipped from Japan, becomes problematic. And when I outgrow basic books, may I sell them to another student? These issues are not contrived, and are not limited to unethical cases. A broad ruling would have potentially harmful effects.
I'd guess that in your case, you'd be buying Japanese materials from Japanese publishers, and then having them shipped (possibly by the publisher themselves) to your country, and that these Japanese publishers don't normally sell their materials in your country.
That would not be a problem. To run into the situation at issue in this case, you'd have to be importing back to your country books that a publisher in your country sold in Japan.
The laws restricting imports are generally aimed at curbing grey market goods. When the good you are importing is one that has no "white market" equivalent in your country, you are probably OK.
I agree that it should work as you describe. But there's always a danger of courts making a broad ruling. The norm seems to be for content purveyors to push for a broad ruling, as it's in their business interest.
Edit: the particulars of the case in the article are not so interesting to me, excepting how it might impact more legitimate uses of 1st sale. I do not support the defendant's actions.