Recent advances in microfluidics technology have led to the emergence of miniaturized biochip devices for biochemical analysis. A promising category of microfluidic biochips relies on the principle of electrowetting-on-dielectric, whereby discrete droplets of nanoliter volumes can be manipulated using an array of electrodes. As chemists adapt more bioassays for concurrent execution on such "digital" droplet-based microfluidic platforms, system integration, design complexity, and the need for defect tolerance are expected to increase rapidly. Automated design tools for defect-tolerant and multifunctional biochips are important for the emerging marketplace, especially for low-cost, portable, and disposable devices for clinical diagnostics. We propose a unified synthesis method that combines defect-tolerant architectural synthesis with defect-aware physical design. The proposed approach allows architectural-level design choices and defecttolerant physical design decisions to be made simultaneously. We use a large-scale protein assay and the polymerase chain reaction procedure as case studies to evaluate the proposed synthesis method. We also carry out simulations based on defect injection to evaluate the robustness of the synthesized biochip designs.