The unifized version of the EPI is only used in the alignment not in the final result. You can repeat the similar steps yourself, but you have to be careful about the order of the matrices and the warps. With afni_proc.py, you get a script that you can use as an example with all the transformations in the necessary order. That includes not only the blip-up/down warps, but also an obliquity transformation, motion correction, alignment to an anatomical dataset and affine and nonlinear alignment to a template. The unWarpEPI.py script includes motion correction and the nonlinear warp to the mid-point between blip-up and down.