The phase of an electron wave is sensitive to the local electrostatic environment and can therefore provide information about atomic-scale structural variations. In electron ptychography, however, specimen thickness, multiple scattering and projected atomic overlap can complicate the quantitative interpretation of the reconstructed phase. Here, we use a twisted trilayer WS2 thickness staircase containing monolayer, bilayer and trilayer regions as an internal reference, with all regions measured under identical experimental conditions. The mean W-column phase increases by approximately 13.2% from the monolayer to the bilayer region, compared with only 4.7% from the bilayer to the trilayer region, revealing a nonlinear thickness dependence. W-S overlap has little effect on the W-column phase, whereas short-range projected W-W overlap increases it by approximately 8-9%. These results provide a benchmark for evaluating quantitative phase measurement in multilayer WS2 and for assessing phase-based mapping of local electrostatic potential, charge-density and three-dimensional atomic-scale polarization.