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PtSe₂ shows prominent layer-dependent electronic and optical properties due to interlayer orbital p_z hybridization between interfacing Se atoms. This indicates that the interactions involved with the interlayer hybridization as well as van der Waals interactions contribute to the stability of PtSe₂, calling for an accurate computational framework to describe these interactions on equal footings. To this end, we employ many-body Diffusion Monte Carlo (DMC) calculations to investigate phase stability and interlayer binding properties of bilayer PtSe₂. We firstly computed the DMC interlayer binding energy curves for bilayer PtSe₂ with various stacking modes. It is found from the comparison between DMC and DFT results that r²SCAN+rVV10 functional outperforms other vdW-corrected functionals in predicting interlayer binding energies and distances, relative stability among different stacking modes, and even band gaps. Finally, using the DMC-benchmarked r²SCAN+rVV10 functionals, we investigate electronic properties of PtSe₂ beyond its bilayer form including its metal-insulator transition, with respect to the layer count.