Maybe they will, but this seems to be separate in that if it resolves the physical address from the code during the checkout process like a DNS call, it isn't reliant on actually shipping with Japan post and even if it does, it now has the physical address, so why not use that.
One thing about the long physical address is that it adds a bit of redundancy. Misspelled or wrong name... still arrives. Misspelled street or city... might still arrive. I'm guessing 1 number off on that code and it's wrong. For the example in the story, a customer inputs the number, three store makes the call to Japan post and renders the physical address to the customer so they can verify before committing.
Surely they won't be so incompetent the specifications won't include a correction code and mandatory checking of it ?