We don't know if it doesn't pertain to the story at this point in time. All we know is that the game that they were going to develop was shelved, but that doesn't mean the content won't be implemented. Hell, it could be in KH3 for all we know.
It was also the big finale to BBS:FM. Otherwise, BBS:FM ends with Aqua fighting the Red Eyes Heartless and that's a hugely disappointing finale. Anyone who gets to the end of BBS:FM probably (hopefully) has enough common sense to realize "hey this is what happens from BBS to the end of KH2". I'll give you that "Birth by Sleep volume 2" is a bit confusing, so I would agree to them removing that.
And you can't entirely argue the point of people wondering why a certain game isn't included because right now, given the ending of 1.5, DDD isn't going to be included in 2.5 either.