New York state currently uses an amended version of the 2015 IRC (
https://codes.iccsafe.org/public/document/toc/446/)
Table N1102.1.2, Zone 5 requires R-20 or R-13+R-5 for wood framed walls.
R105.4 Validity of permit.
The issuance or granting of a permit shall not be construed to be a
permit for, or an approval of, any violation of any of the provisions of
this code or of any other ordinance of the jurisdiction. Permits
presuming to give authority to violate or cancel the provisions of this
code or other ordinances of the jurisdiction shall not be valid. The
issuance of a permit based on construction documents and other data
shall not prevent the building official from requiring the correction of
errors in the construction documents and other data. The building
official is authorized to prevent occupancy or use of a structure where in
violation of this code or of any other ordinances of this jurisdiction.
Is there no sheathing under the house wrap?
I can't speak to the requirements of Energy Star v3.1 but I'd guess what your builder is doing won't pass that either.