This paper presents an investigation of System-on-Chip (SoC) communication latency optimization for 3D system integration and highlights the role of architectural modifications to maximize the Power, Performance, \& Area (PPA) benefits. An instance of a highly configurable RISC-V SoC is implemented using ∼2nm nanosheet technology and different 3D stacking options using design flow from sign-off tools. The proposed implementation targets performance optimization for different 3D partitioning scenarios: Memory-on-Logic (MoL) \& Logic-on-Logic (LoL). We target 2-die 3D Integrated Circuits (3D-IC) with high density 3D interconnect using Face-to-Face (F2F) hybrid bonding (∼1µm), and 3-die stack, as Face-to-Back (F2B) on top of F2F. Our analysis of the 16-core SoC instance shows that the proposed architectural optimizations bring a significant reduction of 4 pipeline stages in the design hierarchy at a marginal cost of 9\% effective frequency loss when implemented in 3D in comparison to the baseline 2D architecture. Further, going from 2D to 3D allows more than 40\% total system wire-length reduction \& 10\% less cell area, resulting in 20\% power savings. These findings hold promise for further explorations on many-core SoC instances (256 \& more) facing system interconnect challenges.