Transparent inks are always used in process inks so that the colors blend to make the other colors. Spot colors may be opaque depending on the pigments. As for the UV lamp settings, I would refer to the ink manufacturers recommendations. Transparent ink may allow slightly more UV radiation to penetrate and reach the photo initiator, but the amount is insignificant. The ink coverage and lightness/darkness of the form will determine the amount of UV energy required to cure the ink.
The Harmony Between Digital Printing and Thermoforming
Developments in inkjet ink chemistry have opened a host of benefits for printers.