Quantum computing has transformative computational power to make classically intractable computing feasible. As the algorithms that achieve practical quantum advantage are beyond manual tuning, quantum circuit optimization has become extremely important and integrated into today's quantum software stack. This paper focuses on a critical type of quantum circuit optimization - phase-polynomial optimization. Phase polynomials represents a class of building-block circuits that appear frequently in quantum modular exponentials (the most time-consuming component in Shor's factoring algorithm), in quantum approximation optimization algorithms (QAOA), and in Hamiltonian simulations. Compared to prior work on phase polynomials, we focus more on the impact of phase polynomial synthesis in the context of whole-circuit optimization, from single-block phase polynomials to multiple block phase polynomials, from greedy equivalent sub-circuit replacement strategies to a systematic parity matrix optimization approach, and from hardware-oblivious logical circuit optimization to potential hardware and fault-tolerant friendly circuit optimization. Our experiments demonstrate improvements of up to 48.58 % with an average total gate reduction of 35.83%-and reductions in the CNOT gate count of up to 40.63%, averaging 27.9%, for logical circuits across a representative set of important benchmarks.