Layer 25 is default layer for 3D outline.
There is no need to add component outline on other layer for bottom side components.
I haven't moved to V9 yet so I can't help there.
Have you assigned the board thickness?
( If not, this could be the reason bottom view is not coming up).
Did you set the geometry.height attribute for all of your parts? Otherwise they show up (in some views) but are flat.