As fabrication processes exploit even deeper submicron technology, power dissipation has become a crucial issue for most electronic circuit and system designs nowadays. In particular, leakage power is becoming a dominant source of power consumption. Recently, the reconfigurable single-electron transistor (SET) array has been proposed as an emerging circuit design style for continuing Moore's Law due to its ultra-low power consumption. Several automated synthesis approaches have been developed for the reconfigurable SET array in the past few years. Nevertheless, all of those existing methods consider fabrication constraints, which are mandatory, merely in late synthesis stages. In this paper, we propose a synthesis algorithm, featuring both variable reordering and product term reordering, for area minimization. In addition, our algorithm takes those mandatory fabrication constraints into account in early stages for better outcomes. Experimental results show that our new method can achieve an area reduction of up to 24% as compared to current state-of-the-art techniques.