Demands to advance toward more resilient and sustainable cities in terms of reducing casualties, economic losses, downtime, and environmental impacts derived from earthquake-induced damage are becoming more frequent. Indeed, accurate evaluations of the seismic performance of buildings via numerical simulations are crucial for the sustainable development of the built environment. Nevertheless, performance estimations could be influenced by alternative probabilistic methods that can be chosen throughout the procedure of building-specific risk assessment, specifically in the construction and validation of fragility functions. This study evaluates the numerical impacts of selecting different probabilistic models on seismic risk metrics for reinforced concrete dual wall–frame buildings. Specifically, alternative probabilistic models are implemented and evaluated for (i) the identification and elimination of unusual observations within the simulated data (i.e., outliers); (ii) the selection and implementation of different Probability Distribution Functions (PDFs) to estimate fragility functions at different limit states (LSs); and (iii) the application of goodness-of-fit tests and information criteria to assess the validity of proposed PDFs. According to the results, the risk measures showed large variability at the extreme building LS (collapse). On the other hand, for a lower LS (service level), the measures remain similar in all the cases despite the methods selected. Further, the variability observed in the collapse response is up to two times that after eliminating data outliers. Finally, the large variability obtained with the evaluated alternative probabilistic modeling methods suggests re-opening the technical discussion over the state of the practice often used in earthquake engineering to improve the decision-making process, mitigating earthquake-induced consequences in an environmentally, economically, and socially beneficial manner.