We combine in situ Bragg diffraction, laser diffraction, high speed fluorescence scanning, and large-scale data processing to arrive at statistically significant conclusions about the role of order during the microchip electrophoresis separation of short DNA molecules (86 base pairs and 709 base pairs) in colloidal crystals. This experimental approach directly connects the presence of long-range order (obtained by laser diffraction) to the DNA transport (obtained by fluorescence detection) in hundreds of "mini-columns" composed of 500 μm-long regions of the devices. To within statistical significance, the electrophoretic mobility is the same in regions of the chip with long-range order and those with short-range order, independent of the electric field and molecular weight. Moreover, the relative mobilities of the DNA agree well with a recent estimate for the Ogston sieving mobility in a colloidal crystal. Similar to previous work, the band broadening during the transit through the colloidal crystal is negligible. These features imply that colloidal crystals for DNA separation in the Ogston sieving regime do not require exquisite control over the microstructure to maximize the separation resolution, simplifying their assembly for routine use.