Public transit systems with high occupancy can save greenhouse gas (GHG) emissions. However, current transit systems had not been designed to reduce environmental impacts. This motivates the study of the benefits of optimal design and operational approaches to reducing the environmental impacts of transit systems. Transit agencies could resort to level-of-service (LOS) changes, for example, reductions in vehicle kilometers traveled. In previous work, we explored the unintended consequences of lowering transit LOS on emissions from a single-technology transit systems. Herein we extend the analysis to account for a more realistic case: a transit system with hierarchical structure (trunk and the feeder lines) providing service subject to demand elasticity. By considering the interactions between the trunk and the feeder systems, we provide a quantitative basis for designing and operating integrated urban transit systems that can reduce GHG emissions and societal costs. We find that large cities may achieve societal cost as well as emission savings by employing a hierarchical structure, while the non-hierarchical structure may be better for small cities. Highly elastic transit demand may cancel emission reduction potentials, yet for mass transit modes these potentials are still significant. Transit networks with buses, bus rapid transit or light rail as trunk transit modes should be designed and operated near the cost-optimal point when the demand is highly elastic, while this is not required for metro.