Nope, The rectifier is a three phase bridge
, all of the three phase AC (including the negative-going part of the sine wave) is used in making DC! Very efficient!
None of the three legs of the alternator go negative with respect to the Bike's ground because there's no ground reference anywhere in the alternator, even the common point of the three phases floats. Thus the negative-going part of the sine wave is referenced to bike's ground thru the negative-rail diodes in the bridge, thus driving the positive-going legs to an even higher output.