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This paper examines the driving forces of urban network formation through the simulation of inter-city transport networks in Southeast Asia. We present a generative network model (GNM) considering geographical and topological effects, thus combining factors commonly analysed through traditional spatial simulation models (e.g., gravity models) and topological simulation models (e.g., actor-oriented stochastic models) in a single framework. In our GNM, it is assumed that the probability of connections between cities emerges from competing forces. Stimulating factors are a measure of city size (i.e., population) and a topological rule favoring the formation of connections between cities sharing nearest neighbours (i.e., transitive effects). The hampering factors are physical distance between two cities as well as institutional distance (i.e., border effects). We discuss the model in the context of on-going engagements between urban-geographical research and the network science literature, and validate the credence of the model against empirical data on the transport networks connecting 51 major cities in Southeast Asia. Our results show that (1) the generated networks approximate the observed ones in terms of average path length, clustering, modularity, efficiency and quadratic assignment procedure (QAP) correlation between the observed composite network and the generated one, and that (2) GNM performs best when topographical and topological factors are considered simultaneously. Each factor contributes differently to network formation, with transitive effects playing the most important role.