Hello
3D Box is the main thing that prevents us from fixing the coordinate system bug. (The second thing are guides, but they're much easier to fix.)
The reason is that it has a design fault - it stores perspectives and faces in desktop coordinates. A simple Y inversion does not fix the problem, because some code (e.g. default face coloring) is dependent on the chirality of the 3D coordinate system, and flipping the Y axis inverts the chirality.
There's also a slew of other bugs related to 3D box in our bug tracker.
What do we do with it in 0.49? I would really like to see the coordinate system bug fixed in 0.49, even if it means rewriting the 3D box from scratch, or even disabling it. Fancy features aren't very useful if we don't get the basics right.
The issue of supporting legacy documents with 3D boxes is separate and I think it can be done if the 3D box gets rewritten first. We would just need to fix the document at load time. Initially I wanted to do this by direct XML manipulation before creating the SP tree, but now I see this has limitations - compatibility code at SP level is probably a better idea.
Regards, Krzysztof.