Grammar books say that “had + PP” is used for something that happened before the past events. i.e. The event that happened before that which happened in the past. Like, “He had refused to narrate what had taken place before he fled to her house,”

Then, how about, “He had said he wanted comfort, not stuffiness”. In this sentence, according to the grammar books, “His saying” comes before “his wanting comfort”, which is logically impossible. How can he say he wanted comfort, before he wanted comfort?

How about this one? “She had seen what happened to me during those Octobers when the Sox tantalized us once again”. How can she see what happened before it happens?

Below are some more examples from COCA.

Definitely I seem to be missing something….

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The client had said he wanted an aggressive campaign.

Mr. Bush had said he wanted a vote in the UN no matter what the whip count.

Mrs. Munson had seen what happened, but she'd left without even changing her surly expression.

And that after he had decided he wanted to marry my mother, he once asked her: " Are you afraid? " And my mother answered: " No, I am not afraid. "

Marta's son Beau, then thirteen years old, had decided he wanted to live with his mother again.
I think this topic ( past perfect) raises more problems for learners than other areas of the grammar in my opinion. I think many experts will agree and have pointed out more than few times here that we should avoid past perfect if the contexts can be narrated clearly without this use; especially when contexts involve the use of conjunction (i.e.while ,before, after, when, as, and during ). Just like this one:
pructus“He had refused to narrate what had taken place before he fled to her house,”
That said, you have a double past perfect construction, which is a mouthful and not necessary, that my opinion.
He refused to explain what happened before he fled to her house. I think the meaning is clear with a simple past construction.
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 Terryxpress's reply was promoted to an answer.
Thanks dimsumexpress!!

It's really difficult to get a grasp on what native speakers's sense of past perferct is.