Are clear lenses legal on rear stop/turn/tail lights?

Yes. The Federal Motor Vehicle Safety Standards clearly state that measuring the performance and color of a lamp assembly is done with the light source energized.  There is nothing illegal or non-compliant about red or yellow LEDs behind a clear lens, as long as the effective color of the light when illuminated is red or yellow, per SAE J578C requirements as specified in FMVSS-108.