Firearm examination is subject to increased scrutiny regarding its foundational validity and inherent subjective nature. The increased use of automatic comparison systems may help to reduce subjectivity. In this paper, we present the performance and limits of an automatic comparison system that assigns a weight to the forensic findings for the comparisons between firing pin marks, breechface marks, or a combination of the two. This weight is expressed by a likelihood ratio (LR) based on 3D topographical measurements coupled with a bi-dimensional statistical model. As the performance of such systems may depend on the reference databases used to inform the model, we investigated the impact of the brand of ammunition and the number of samples. We show that reference databases used to calculate LRs should ideally consist of the same type of ammunition as is seen in the case under investigation and that 7 specimens fired by the same firearm are enough to obtain rates of misleading evidence of a similar magnitude compared to those obtained when far more specimens (60) are used. Additionally, the automatic system was used to assess the outcomes of 7 cases with known same-source or different-source ground truths. These cases were also examined by 8 qualified firearm examiners. In all cases, the experts' appraisals were in line with the ground truth. The automatic system showed some limitations in cases were the data were not sufficient to calculate a robust LR, but also that it can assist and enhance the examiners in their decision process.