Maybe it's better to describe the core problem:

I have an atlas in MNI space (sampled at 1.5 mm)
  /path/to/aal_atlas.nii
and a set of inverse warp parameters to put it in native space of a T1 image: (sampled at 1 mm)
  /path/to/iy_T1.nii

If I call a script that sets
  matlabbatch{1}.spm.spatial.normalise.write.subj(1).def = {'/path/to/iy_T1.nii'};
  matlabbatch{1}.spm.spatial.normalise.write.subj(1).resample = {'/path/to/aal_atlas.nii'};

and then run
  spm_jobman('run',matlabbatch)

my would-be native-space atlas has dimensions 79x95x79 and voxel size 2x2x2 mm.

Neither the bounding box nor the voxel size make sense?
The example scripts I know automatically use the T1's settings - why not now?

Many thanks!