Thanks to Doug Baird* from NOAA for explaining the situation. This is from an email he sent me yesterday.
The large amount of overlap with the PDBS (Phase Differencing Bathymetric Sonar) data collected by USGS in Cape Cod Bay was intentional. This is the first year that Coast Survey has tried using PDBS in a production mode - all previous uses of PDBS was for test and evaluation purposes - and we have yet to ingest any PDBS data into our charting pipeline. So, we wanted to get as much of a sample size of corresponding data from a known multibeam system as we could to determine the capability of the USGS PDBS and if we could use it to disprove charted features such as wrecks, rocks, and obstructions. All previous experience with our test PDBS systems has lead us to believe that a PPDBS may meet IHO Order 2, but definitely not IHO Order 1 - which is our normal standard.
*Chief, Operations Branch, NOAA, Coast Survey, Silver Spring, MD