In this work, the substrate holders of three principal geometries (flat, pocket, and pedestal) were designed based on E-field simulations. They were fabricated and then tested in microwave plasma-assisted chemical vapor deposition process with the purpose of the homogeneous growth of 100-μm-thick, low-stress polycrystalline diamond film over 2-inch Si substrates with a thickness of 0.35 mm. The effectiveness of each holder design was estimated by the criteria of the PCD film quality, its homogeneity, stress, and the curvature of the resulting “diamond-on-Si” plates. The structure and phase composition of the synthesized samples were studied with scanning electron microscopy and Raman spectroscopy, the curvature was measured using white light interferometry, and the thermal conductivity was measured using the laser flash technique. The proposed pedestal design of the substrate holder could reduce the stress of the thick PCD film down to 1.1–1.4 GPa, which resulted in an extremely low value of displacement for the resulting “diamond-on-Si” plate of Δh = 50 μm. The obtained results may be used for the improvement of already existing, and the design of the novel-type, MPCVD reactors aimed at the growth of large-area thick homogeneous PCD layers and plates for electronic applications.