AFNI does not warp these oblique datasets on-demand one way or the other. The GUI uses the cardinal equivalent of the data as it is stored without any transformations. While viewing the data, you no doubt saw the warnings about dealing with oblique data and using 3dWarp. Using 3dWarp, as you have used it, is the recommended way to transform and view the data. For more precise alignment, you may also use align_epi_anat.py, which will match obliquity (using 3dWarp) and register the EPI and anatomical datasets.
