どうもPractical English Usageの日本語版なんて読んじゃったから
妙な勘違い起こしてるっぽい。普段使ってるForestとかの日本の
受験参考書と説明のしかたが違うから、それで変にこじらせちゃったのかな。

Practical English Usageの該当部分：

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2. meaning and use: earlier past
The basic meaning of the past perfect is ‘earlier past’. A common use
is to ‘go back' for a moment when we are already talking about the past,
to make it clear that something had already happened at the time we are
talking about.

During our conversation, I realised that we had met before, (not ... I
realised that we met before or ... have met before.)

↑これ大過去の用法。

5 how long? past perfect, not simple past.
We use a past perfect, not a simple past, to say how long something had
continued up to a past moment. A simple past perfect is used with 'nonprogressive
verbs’ like be, have and know.

She told me that her father had been ill since Christmas.
(not ... that her father was ill since Christmas.)

↑これ継続の用法。
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当然、大過去と継続は別物。