I understanding what you're saying. You're talking about how odd it is to sell both the single discs and the box set so close to each other, right? I kind of thought of that too when they did the same thing with the Diamond and Pearl seasons. As others have mentioned, Pokemon is still popular and successful with its DVRAB so Viz could do something like this and they would still get a nice sum of money. Some people might want to go straight for the singles, even though the set gives them the same episodes, or it's there in case the sets run out and people could buy the singles.
Plus, I do remeraber how the episodes for Advance were released on singles first and then on two box sets.