When I tried to use 3dWarpDrive to align a NifTI file to an AFNI BRIK file or vice versa, 3dWarpDrive would warn about the mismatch in grid offset.
This is weird because both files are generated by td3d with identical parameters except output format. I could even see the two offset being identical in base and input. 3dvolreg and 3dAllineate don't have this misbehavior.
