OK it’s been a while but I’m looking into this issue again. I think I resolved the problem but wanted to update this post in case somebody else encounters the same thing. It’s a little confusing why this is the specific symptom, but if you swap the x-axis of the transform before applying, the x-axis shrinking no longer occurs:
mrconvert standard2acpc_dc.nii.gz tmp-[].nii -force
mv tmp-0.nii x.nii
mrcalc x.nii -neg tmp-0.nii -force
warpconvert tmp-[].nii displacement2deformation mni2acpc_mrtrix.nii.gz -force
rm x.nii tmp-?.nii
tcktransform mytracks.tck mni2acpc_mrtrix.nii.gz mytracks_mni.tck -force