Mj, your concerns would be covered by the owners representatives, i.e. A/E.
The punch lists and close out documentation would guarantee design compliance, the contractors final payment and retainage would be held until all close outs were satisfied.
An AHJ is treading on thin ice as far as demanding item for item installation beyond code and holding up a C.O.
If there are added items, the AHJ has every right to ask for new drawings to review, if there are deletions, the AHJ would also have the right to ask for "record drawings" but not to turn down a job.
BTW, this is only MO.
Roger
