Current dose calculations for permanent prostate implant brachytherapy are performed using the American Association of Physicists in Medicine TG-43 formalism, where dose distributions are derived for a homogeneous water phantom in the absence of inter-seed effects. Using a model-based approach, this study investigates differences in dosimetry, radiobiological endpoints, and clinical outcomes, compared to the clinical TG-43 formalism. Post-implant CT images are used to derive unique virtual patient phantoms (water- and tissue-based) for a cohort of patients. With the use of the Monte Carlo (MC) approach to dose calculations, radiation transport and dose deposition is simulated in these virtual phantoms. Dose and volume metrics are extracted for all the patients and comparisons between the tissue- and water-based approaches are made. Dosimetric quantities are shown to vary between the tissue- and water-based approaches for the prostate and organs-at-risk, with dose overestimation of up to 9.12% in the prostate using the water-based approach.