Transparent toners are good for making pearl or metallic colors. This way you can see the flake inside the transparent color.
If you used a nontransparent toner (or color), the flake is not as noticeable.
The way it works is when you spray a regular metallic or pearl color (like on factory automobiles, you will actually see through the paint color (toners) into the flake, thus making the flakes appear the same as the color they are in. Make sense?
For example, lets say you have a bucket of water (transparent toner), and you placed your hand holding a mirror (flake) in it, well you can see the mirror in the water. Now take do the same, but place the mirror in a muddy bucket of water (non-transparent toner), you do not see the mirror (flake).
WOW- A crude example, but the fastest one I could think of.
Hope this helps!