The main purpose of the 3D preview is to be able to spot issues in registration between back and front and between any other print layers in the design.
If you have white in a color layer in a PDF file, it doesn't show up as transparent in the previews of the Arizona Xpert Engine.
The use of built-in Arizona Xpert Engine features such as the white/black/varnish image masks results in a more accurate preview than the use of special ink mapping configurations in the print mode and files that include both color and spots mapped to special inks. The use of built-in Arizona Xpert Engine features enables you to check the opacity of an application - i.e. based on the number of white or black layers.