Warranty coverage costs a lot of money, especially in a country like Japan. If you want 1-year warranty or 3-year warranty (boxed sets), then you have to pay the price for that.
I don't know, personally I haven't had a single bad experience with any hard drive. I've got Seagate, WD and Samsung in my rigs. The last desktop PC I threw away lasted for 9 years with its WD hard drive still in perfect working condition.
I am not sure if they have any "extra" QA/QC checklist for "bulk" (NOT BOXED) HDDs sold in Japan although that is quite common for other commodities imported to Japan (brand clothes in particular). In any case, these "bulk HDDs" in Japan are made by the big players such as Seagate, WD, Hitachi, Samsung, Toshiba. And although they lack the "box", they certainly are brand-new and properly packed.
Momay, I'm not sure if you can even do RMA to manufacturer for brand items "handled as bulk." AFAIK, for instance in popular DIY store like T-Zone and Clevery in Akihabara, after the store's own limited warranty for a certain bulk item, or a "special store item" expires, that's it. But then again what are the chances of total failure in 3 months anyway? Well, for a 17,000 yen 1TB hard disk drive, that may or may not be worth the risk depending on your situation.