Is there a document describing the actual physical format for a Unidata netCDF file?
Yes, the NetCDF User’s Guide contains an appendix that specifies the netCDF file format. Also, the “NetCDF File Structure and Performance” chapter explains the physical structure of netCDF data at a high enough level to make clear the performance implications of different data organizations. If users only access netCDF data through the documented interfaces, future changes to the format will be transparent.