Yes, these features are expected. For 3D acquisitions the images are reoriented to be roughly orthogonal with the NIfTI space (e.g. sagittal and coronal acquisitions are losslessly reoriented to axial slices). This should have no influence on tools like SPM (which read the SForm and QForm rotation matrices) but does provide more consistency for simple viewers that ignore these transforms. So the image data is reoriented and therefore the dimensions and rotation matrices are adjusted to reflect this orthogonal realignment. Despite the fact that the headers look different, if you use SPM's "DISPLAY" button will show they are still in register with each other. This helpful feature is only applied to 3D acquisitions (T1 MPRAGE, T2 SPACE, etc), 2D acquisitions (EPI-based fMRI, DTI, etc) are not reoriented because the current slice timing tools assume that the order of slices stored on disk matches the acquired slices.