I also agree with the inspector writing citations for violations they see. In this case, the things she noted were in plain view. She didn't go snooping or anything. But like emahler said, what if the HO can't/won't pay for the fixes? Hanging the extra work on my permit is just not right.
When the inspector first called me and laid all this out, my attitude was "Fine, don't close the permit. My work passed inspection, and I've been paid." I'm not sure what the ramifications would have been, but I suspect nothing would have happened. My experience with the city is that when a permit expires, they just cancel it and forget it.
But the city stopped doing permits/inspections for electrical work a year ago, so now we have the state as the AHJ. They do things differently. I recently had a permit for a kitchen remodel approach the one-year expiration date, and I was having trouble getting a hold of the HO to schedule the final. I called the inspector and asked how to proceed, and he told me if the permit expired without a final, I'd have to pull a fresh one. Meanwhile, the inspector could order a disconnect. I was able to get the HO on the phone and get the kitchen inspected recently, so it all worked out. I'm glad it turned out the way it did, as the HO is a state senator, so I imagine there might have been complications.