First off, get a GeoTiff file and use it to build a simple join new aggregation. Does it work?
My guess is that it will not because the current GDAL handler keeps the GDAL handle open once it reads the information needed to build the DDS/DMR so that it can be used for a data response. This breaks the NCML handler (at least it does for HDF4).
We need to complete this by June 2017
The issue noted above - that the gdal handler kept the GDAL Handle open so it could be used by subsequent calls was fixed by this ticket.