Your comments parallel 
  https://github.com/rordenlab/dcm2niix/issues/438
I hope to release a new stable release soon that should do a better job detecting different 3D acquisitions. While people find it convenient to losslessly re-orient their images to axial slices, we need to be careful not to reorient EPI scans, otherwise we would disrupt slice timing. I try to err on the side of caution, to protect your data.

With fsleyes, you can open the View Settings window and set the "Display Space" to be "World Space". Perhaps you can contact the FSL team to see if there is a way to make this the default behavior.

If you are planning a large re-conversion, you might want to wait until the next stable release of dcm2niix. Depending on your manufacturer, you may get richer meta data.