I voted to close this question as off topic because it seems to me that the question is primarily about the common practice in bookstores in Japan and that the language plays only a marginal role in the question. But the language seems to play at least some role here. Is this question on topic or off topic? Can we distill some criteria which are applicable to the future questions?
I'll repeat my comment here: There's currently no other place to pose this arguably interesting and helpful question and it's not blatantly off-topic, just borderline. I think we'd do well to include it in the scope of this site.
I'm also inclined to agree that the question is borderline, but it is also pretty closely tied to language as I see it as possibly being related to how words are organized in a dictionary though with a bit more in the way of nuances to it. Likewise, if we apply the removal of the linguistic aspect from the questions I don't see how the question can be phrased since organization of books does tend to be a language specific topic.
Also, one thing to note about the question, it is what could be considered a bit of a one off in that once it is answered an entire class of questions can be covered by it when it comes to duplication. Finally, it is likely extremely useful to most novices of the language in that it cannot be readily answered though most basic book exercises.
I am happy to admit that when I asked the question I was fully aware that it might be controversial and be at the edge of our topic boundary. But since the site is in its infancy and that boundary is not well defined, indeed our faq says nothing, that it would be well worth asking to help clarify what is on and off topic, even if it means sacrificing some of the old hard-earned reputation (-:
Plus I've really wanted to know the answer to this question for years and in this case even my Japanese friends haven't really helped.