Usually WC clowns of any species are cheaper than TR clowns. So that's not a factor.
WC clowns, especially percula, are very susceptible to a disease called Brookynella for about the first month, which can be difficult to treat. You rarely have that problem with TR percs.
Vibrance of color in percs in a little bit genetic and a lot a bit about what you feed them. There are several hatcheries that feed very high quality foods with high levels of astaxanthin from the start. It would be very difficult if not impossible to tell the difference between these fish and wild fish. There are other hatcheries that pump out large volumes of fish and it is very easy to see by their color that they are TR fish. Usually these fish can regain their vibrance if you feed them high quality foods. (Rod's Food, Formula 1, cyclop-eeze)
The biggest concern that I see with TR fish are the head and gill cover deformities that you see in fish from hatcheries that don't pay attention to detail.
The good news is, hatcheries that have vividly colored fish don't have as big a problem with head and gill deformities, but you still have to choose carefully. The deformities don't affect the fishes health, but they are unsightly IMO.