This study investigates the impact of rotation axis configuration and modulation of tube voltage (kV) and dose rate on organ dose estimates in dental panoramic radiography, using Monte Carlo simulations. Computational phantoms representing 15 year-old male and female patients were each exposed to 16 protocol scenarios across three panoramic radiography units, varying the rotation centre (sliding versus fixed) and the presence or absence of x-ray beam modulation. Simulations were conducted using the particle and heavy-ion transport code system code, employing dump files and a multi-source approach to replicate realistic exposure conditions. Results were expressed and analysed as percentage differences relative to reference protocols incorporating a sliding rotation centre and beam modulation. The findings revealed a consistent and substantial underestimation—up to 50%—of doses to the thyroid, salivary glands, and brain when fixed-axis or non-modulated protocols were applied. The oral mucosa (lips and chin) exhibited marked overestimation (up to 700%), particularly in males, attributable to mandibular anatomy and beam geometry. Sex-related differences were evident in doses to the tongue and floor of the mouth, linked to anatomical mass variations, with male tongue mass approximately 8% greater than female. All results displayed relative errors below 5%. These findings highlight that simplified simulation models lacking a sliding rotation axis and beam modulation significantly distort and compromise dose assessments. Consequently, realistic modelling of beam dynamics is essential for accurate dosimetry in panoramic radiography.