I'm not suggesting to change it to use log at each site. However, the scaling that Phred employs is meaningful; specifically for Phred = x * 10, x in Z (set of all integers), Psuccess = 1 - 0.1^x, Perr = 0.1^x. Since the scaling is applied uniformly, Phred scores can be used equivalently to log probabilities, IIRC.