1. A method for designing a system on a target device, the method comprising: identifying a partition having a plurality of instances in the system from an extraction netlist, wherein the partition implements a component from the extraction netlist and each instance of the partition implements an identical component having a same functionality as the component, wherein identifying the partition comprises identifying an initial partition, and expanding the initial partition, wherein expanding the initial partition comprises building a merge set, identifying a merge from the merge set having a highest savings in cost relative to other merges from the merge set, and applying the merge identified with the highest savings in cost; performing synthesis optimizations on the partition to generate a synthesis optimization solution; and applying the synthesis optimization solution for the partition selectively to the plurality of instances of the partition in the system, wherein at least one of the identifying, performing, and applying is performed by a processor.