Yes. You stated the following in your original post:
Enigma wrote:a) I (had) shouted at Dave before I hit him.
An anomaly can exist with these conjunctions--though you may not be aware of it because natives intuitively apply verb tenses and aspects:
b) "Before the storm had ended but after the worst was over, the captain radioed for help."
One may think that the tenses and aspects should be identical to sentence a--that the past perfect doesn't belong in the 'before' clause, but rather in the main clause, because the 'ending' happens after the captain radioed.
But, in sentence b, the function of the past perfect is similar to that of the present perfect in sentences in the present tense; that is, the past perfect shows completion rather than time sequence.
You acknowledged that time sequence is not necessarily the deciding factor.
1. He
refused to go until he
saw all the pictures.
2. He
refused to go until he
had seen all the pictures.
3. He
had refused to go until he
saw all the pictures.
4. He
had refused to go until he
had seen all the pictures.
In each case the refusing precedes the seeing. But any of the above four sentences is permissible, depending on the overall context.
In sentence 2, the choice of tenses is the opposite of what one would get by adhering strictly to time sequence. As you rightly said, the past perfect is used here to show completion.
I agree with much of what you say, but I think where we differ is that you are trying to derive tense/aspect rules for a complex sentence
without looking outside that sentence. Look at the main clauses of the four sentences listed above. How can the subordinate clause help you to decide whether to say "refused" or "had refused" in the main clause? It can't; you have to look outside the sentence, at the overall context, to decide that.