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Pair atomic density fitting (PADF) is a promising strategy to reduce the scaling with system size of quantum chemical methods for the calculation of the correlation energy like the direct random phase approximation (RPA) or second-order Møller-Plesset perturbation theory (MP2). PADF can however introduce large errors in correlation energies as the two-electron interaction energy is not guaranteed to be bounded from below. This issue can be partially alleviated by using very large fit sets, but this comes at the price of reduced efficiency and having to deal with near-linear dependencies in the fit set. In this work, we introduce an alternative methodology to overcome this problem that preserves the intrinsically favourable scaling of PADF. We first regularize the Fock matrix by projecting out parts of the basis set which gives rise to orbital products that are hard to describe by PADF. We then also apply this projector to the orbital coefficient matrix to improve the precision of PADF-MP2 and PADF-RPA. We systematically assess the accuracy of this new approach in a numerical atomic orbital framework using Slater Type Orbitals (STO) and correlation consistent Gaussian type basis sets up to quintuple-$ζ$ quality for systems with more than 200 atoms. For the small and medium systems in the S66 database we show the maximum deviation of PADF-MP2 and PADF-RPA relative correlation energies to DF-MP2 and DF-RPA reference results to be 0.07 and 0.14 kcal/mol respectively. When the new projector method is used, the errors only slightly increase for large molecules and also when moderately sized fit sets are used the resulting errors are well under control. Finally, we demonstrate the computational efficiency of our algorithm by calculating the interaction energies of non-covalently bound complexes with more than 1000 atoms and 20000 atomic orbitals at the RPA@PBE/CC-pVTZ level of theory.