Both of them are correct depending on the situation. In the first one, as you said, the "before-after" relationship between events is emphasised. In the second one, there's no such thing.
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goronskyYesterday he had gone to the supermarket.(Does the sentence above mean 'Yesterday he had 'already' gone to the store before doing some other activity'?)Yes. That's why it's a rather pathological example standing on its own.