A few years ago we did not collapse layers and it led to lots of complaints an inefficiencies. Therefore, I would recommend to keep using the collapsed format and use these code snippets to retrieve metadata and pixel data of segments: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_information_from_segmentation_nrrd_file_header
If this does not work for you then you can submit a feature request to issues.slicer.org asking for adding a flag to the storage node that can disable automatic collapsing on save.