3 Layers Toyota Touch-up?
 

I ordered some touch-up paint from Toyota for Raven (D4s) and was given 3 bottles of paint: base coat, top coat, clear coat.

Both the top coat and clear coat are clear. Is the top coat essentially a clear coat, and was I give an extra clear coat?

Sorry for the ignorance

My G1U (silver) Subaru branded touch up paint kit has only clear coat and the silver pigmented base.

On the other hand the touchup kit for my red Honda VFR has a true base coat (which is white), a pigment coat (red), and clear coat.

It's possible that what you're calling a top coat has a separate function, because of what color your car is. It might be to increase the "depth" of the black base.

Interesting. Though, I thought it was odd that I could only find a base coat and clear coat when searching online for my color.