The normalization of electropherograms is required as slower moving peaks generate a wider peak width than the faster moving peaks. The area of any peak is a function of both its peak width and height.
This must be performed on most CE runs because the first migrating peak will be understated in area and late migrating peaks will be overstated. This is due to the fact that faster moving peaks spend less time in front of the detector beam then do the slower moving peaks.
This is only important when making comparisons in concentration between analytes. If you are performing an assay and your migration time does not vary, it is not relevant. This can be referenced in Altria KD, Chromatographia, 35 1993 177-182 “Essential peak area normalization in Capillary Electrophoresis”.