Understanding the electronic structure of mixed-dimensional heterostructures is essential for maximizing their application potential. However, accurately modeling such interfaces is challenging due to the complex interplay between the subsystems. We employ a computational framework integrating first-principles methods, including GW, density functional theory (DFT), and the polarizable continuum model, to elucidate the electronic structure of mixed-dimensional heterojunctions formed by free-base phthalocyanines and monolayer molybdenum disulfide. We assess the impact of dielectric screening across various scenarios, from isolated molecules to organic films on a substrate-supported monolayer. Our findings show that while polarization effects cause significant renormalization of molecular energy levels, band energies and alignments in the most relevant setup can be accurately predicted through DFT simulations of the individual subsystems. Additionally, we analyze orbital hybridization, revealing potential pathways for interfacial charge transfer. This study offers new insights into hybrid inorganic/organic interfaces and provides a practical computational protocol suitable for scaled-up studies.