Bicycle shorts are designed to be worn next to your skin. The construction of the "chamois" has been refined over numerous years to incease the comfort of the rider.

Why would you want to take a product, not designed for use in cycling, and use it in a way that tends to defeat the purpose of the expensive, purpose designed cycling shorts you bought.

If a base layer under cycling shorts was actually a good idea, you can be sure that Assos, Pearl Izumi, et al would be selling them.