Some powders will blend together nicely to make color variations, and others will just appear as separately colored splotches. It has a lot to do with the formulation chemistries. It can also depend slightly on other factors such as particle size and pigment variations.
When you have two incompatible chemistries (urethanes and acrylics are especially bad when mixed with epoxy or polyester-hybrids), you will most likely see craters and other surface defects. This is because certain powders flow out at different speeds, which is one reason the manufacturer recommends a specific cure time and temperature.
If you put compatible powders into a bag and shake them up, the pigments just may be similar enough to produce a blended color. Microscopically you may still see them as tiny dots because that's just the way dry-blended powder coatings work.
Or sometimes you want that mottled appearance... try blending about 10% of a sand-textured coating into a smooth coating and you should see the difference in the flow characteristics of the powders. Orange texture inside a clear is a really cool look
