There may be occasions where it is necessary or desirable to use any one of the possible combinations of past and past perfect, so I would not call it a rule. Nevertheless, the "rule", such as it is, does apply equally to before , after , and by the time , in my opinion. Patterns in which both clauses are in the past perfect seem particularly awkward to me.
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What do you think about patterns with both clauses in simple past?They are among the most useful, I think, and they sound quite natural. See previous post.