As far as I understand, the most important function of past perfect is to refer to 'earlier past'.
However, when I found the following sentences, I couldn't undertand the usage of past perfect, since the action of past perfect tense in the main clause obviously occurred later compared to the action of past tense in the subordinate clause.
Since I have often seen such sentences with above unexpected past perfect, I wonder if natives might have the usage that they use intentionally 'past perfect' tense instead of 'simple past' just to emphasize the image of 'completion, or experience', which doesn't mean the 'earlier past'.
Followings are the common ones in the same category in my question, I think, and, of course, I don't ask you to analyze all of them;
1. "A group of students from the drama college were sitting anxiously in the emergency room in the local hospital. Becky, one of their fellow students, had been run over by a van and the doctor was examining her. < When the van hit her she had fallen heavily and been knocked out. > An hour later, the doctor finished the examination, and they were told that Becky had no major injuries."
2. "Finally, they were able to come back to Auckland. Two years 'had passed' since the boys 'were washed' away from Auckland. Yet, all 15 boys grew up to be fine young men after their adventures at sea."
3. Dick was not a very good swimmer andhadn’t ridden a bicycle since he was six years old.
4. The site was originally occupied by a house, which had been destroyed during a bombing attack in 1945.
5. The frustrated interrogator was not going to give up easily. “Are you both still working in the company?” Barbara, appearing not the least disturbed by the woman’s incontinent insistence, scooped the last cherry out of her dish, smiled, looked directly at her, and said in the identical tone of voice, “We’ve separated, but the company is unaffected.” That shut her up. Barbara had shown her big winner’s badge by using “The Broken Record” technique, the most effective way to curtail an unwelcome cross-examination.
6. Oxygen, key to life on Earth today, began to appear on the planet millions of years earlier than scientists had thought.
6. The training staff was instructed neither to give handouts before the sessions nor to distribute the manuals until after the seminar had ended.