Maybe I missed something in there, but who is verifying any actual performance requirements are being met? All I am seeing is that the owner, contractor or whoever is signing the paperwork is the one that is taking on any risk of not being in compliance should something come up at a later time.
Inspectors are supposed to verify. ComCheck is the software usually used to verify designs meet the energy code. I think the DOE realizes that installed systems don't always match the blueprints, and they often don't meet the code. The latest versions of ComCheck print off a "inspection check list" along with the compliance certificate. See the attached form.
The software also reports all results back to the DOE, so anytime in the future, they could go to any address and verify the installed systems match the design.
As far as responsibility goes, if a contractor installs a system that doesn't meet code, I think that could come back to bite you. And I've been told there is no statute of limitations on this stuff. If someone sells a building 20 years down the road, and the new owner finds out a contractor installed a system that didn't comply with the code, they could come back after the contractor.
Of course, some of that may be exaggerated by the State Employees who are trying to get as much federal money as possible.