My take on this is that you have to look more broadly to understand the tendency for cluttered design in Japanese interfaces. Walk around a small neighbourhood in Tokyo and you'll see how cluttered the layout is. On small "roji" (back alleyways), Japanese like to stack potted plants outside their front doors in a pretty disorganized arrangement. Streets are generally not straight, neighbourhoods rarely follow a grid layout.
(Shimokitazawa is probably the best example in Tokyo of this: http://globalvoicesonline.org/2009/11/04/japan-debating-the-... )
It's the same thing with cluttered interface design, except that whereas in urban layout it produces something amazingly complex, intricate and fascinating to explore, in UI design it just results in frustration and inefficiency. But I'm convinced the two come from the same source, and that you can't entirely separate them.
The beautifully designed interiors you mention come from a completely different place (mentally, not physically). I don't quite know how to reconcile the fact that the two come from the same country/culture, but I do believe they have both been here for a long long time. It's just that software somehow tends to bring out the former, whereas monozukuri brings out the latter.