Using the clear OR white WILL affect your end color that you overlay. Play with different beads, and you will see how indeed, it does.
The hassle of then later coating the base bead, gets when you have to go the the near mandrel area's. It's a little tedious to coat there and retain or rebuild a nice 'pucker' and not let a opal color bleed out. For this reason, I think a clear is better unless you are looking for the colored back to affect the canvas.
It remains personal preferences, but it is still a way to be more frugal with the more expensive colors or one you have little of and need to stretch it out.