Some things may done a bit different in different areas.
I work in IL and I don't know if I ever seen the water heaters jumped. I understand the reason but it is just not done here. Maybe 1/2 the towns require ark faults depending on the code version. If they use NM instead of EMT they probibly don't have a strict code and may be and outdated version. The job might not be too much worse then the other new homes in that town.
I would not think the inspector would look for GFI outlets until the final. You did not say what was wrong with the service grounding. The combo inspector might not know enough about box fill.
It sound like a do-it-yourselfer got a do-it-yourselfer quality house.
