There are advantages both physical and cosmetic. Certain colors and textures are only available in a specific chemistry. For example if you use a Urethane color as a base and an Epoxy clear you will get a Urethane only color which has a lower hardness, and then an Epoxy which is about the hardest available. However Epoxy is not UV stable and will fade and brake down before say TGIC polyester would. Let us not forget that you can make the finish look deeper like a fine paint with the use of clear and it will also alter the shade just a bit.There are addatives that can give affects to the finish like prism powders and irredesent powders which mix nicely into the clear and then seem to be suspended above the color.
Mainly for the hobbiest it's personal preference.Usually based on appearence.
Confusing yet?
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