3drefit modifies the AFNI header information and really is only meant to work on AFNI format datasets. For NIFTI format datasets, it only changes the AFNI extension with the file. The modified AFNI field may be duplicated within the NIFTI fields, and those (the NIFTI fields) will usually have priority. For similar kind of control of the NIFTI fields, use the nifti_tool program instead, or use an AFNI file as an intermediate as you planned.