After" and "before" contain precise information about the sequence of events (what happened first and what afterwards), so we don't need to use past perfect for the action that happened first. We can use past simple in both clauses:
She ate after I left (past simple)
She ate after I had left (past perfect in the subordinate "after" clause).
She left before I telephoned (past simple).
She had left before I telephoned (past perfect in the main clause).