Recently proposed ambipolar nanotechnologies allow the development of reconfigurable circuits with low area and power overheads as compared to the conventional CMOS technology. However, using a conventional physical synthesis flow for circuits that include gates based on reconfigurable FETs (RFETs) leads to sub-optimal results. This is due to the fact that the physical synthesis flow for circuits based on RFETs has to cater to the additional gate terminal per RFET transistors. In the present work, we explore three important verticals that lead to an optimized physical synthesis flow for RFET-based circuits with circuit-level reconfigurability: (1) designing optimized layouts of reconfigurable gates, (2) utilize special driver cells to drive the reconfigurable portions of a circuit, and (3) optimized placement of these reconfigurable parts in separate power domains. Experimental evaluations over EPFL benchmarks using our proposed approach show a reduction in chip area of up to 17.5% when compared to conventional flows.