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We propose hardware-efficient schemes for implementing logical H and S gates transversally on rotated surface codes with reconfigurable neutral atom arrays. For logical H gates, we develop a simple strategy to rotate code patches efficiently with two sets of 2D-acousto-optic deflectors (2D-AODs). Our protocol for logical S gates utilizes the time-dynamics of the data and ancilla qubits during syndrome extraction (SE). In particular, we break away from traditional schemes where transversal logical gates take place between two SE rounds and instead embed our fold-transversal logical operation inside a single SE round, leveraging the fact that data and ancilla qubits can be morphed to an unrotated surface code state at half-cycle. Under circuit noise, we observe the performance of our S gate protocol is on par with the quantum memory. Together with transversal logical CNOT gates, our protocols complete a transversal logical Clifford gate set on rotated surface codes and admit efficient implementation on neutral atom array platforms.