The comprehensiveness of scenarios for the safety assessment of nuclear waste repositories has been studied from many perspectives. In this paper, we offer a generalized interpretation thereof through an explicit quantification of residual uncertainty, which makes it possible to derive conclusive statements about the safety of the repository. To support the operational evaluation of comprehensiveness, we develop a probabilistic methodology which uses set inclusion to capture epistemic uncertainties and propagates these in Bayesian networks to obtain bounds on the probability that the reference safety threshold is violated. We also present analyses which can help in achieving comprehensiveness and describe a novel algorithm for the efficient selection of computer-simulation inputs. The methodology is illustrated with a case study on a near-surface repository in Belgium.