Model-based systems engineering approaches are commonly used to develop safety-critical mechatronic systems. Recently, a new SysML-based method for the dependability analysis of Unmanned Aerial Vehicles (UAVs) has been introduced. The method consists of three main steps: (i) creation of a structural SysML model using building blocks from the underlying UAV dependability profile that extends the model with block-level reliability and time properties, (ii) transformation of the semi-formal SysML model into a formal Dual-Graph Error Propagation Model (DEPM) that captures relevant structural and behavioral properties of the system, (iii) DEPM-based evaluation of system dependability metrics using Markov chain models and state-of-the-art probabilistic model checking techniques. This paper describes the practitioner experiences and lessons learned after the application of the aforementioned method to a sophisticated real-world embedded fault-tolerant inertial navigation system. The case study revealed two particular limitations that have been overcome by the optimization of the method against the state-space explosion of underlying Markov chain models and the introduction of a new computation algorithm for DEPMs with realistic extremely low fault activation probabilities.