A relatively novel approach of autonomous navigation employing platform dynamics as the primary process model raises new implementational challenges. These are related to: (i) potential numerical instabilities during longer flights; (ii) the quality of model self-calibration and its applicability to different flights; (iii) the establishment of a global estimation methodology when handling different initialisation flight phases; and (iv) the possibility of reducing computational load through model simplification. We propose a unified strategy for handling different flight phases with a combination of factorisation and a partial Schmidt–Kalman approach. We then investigate the stability of the in-air initialisation and the suitability of reusing pre-calibrated model parameters with their correlations. Without GNSS updates, we suggest setting a subset of the state vector as ‘considered’ states within the filter to remove their estimation from the remaining observations. We support all propositions with new empirical evidence: first in model-parameter self-calibration via optimal smoothing and second through applying our methods on three test flights with dissimilar durations and geometries. Our experiments demonstrate a significant improvement in autonomous navigation quality for twelve different scenarios.