Traffic models based on the Macroscopic Fundamental Diagram have great potential for future applications of large-scale estimation and monitoring of exhaust emissions. These traffic models offer an aggregated representation of the traffic dynamics in the network, considering mean spatial speeds and average travel distances per zone in the city, which are then used to determine the exhaust emissions using a macroscopic emission model. This aggregated estimation of the travel emissions has an inherent bias when compared to a benchmark scenario consisting of a microscopic estimation of the emissions at the network level. This paper analyzes this discrepancy qualitatively and quantitatively. As our testbed, we consider the traffic data of the 1st of November collected by the project pNEUMA in downtown Athens, Greece. The benchmark scenario consists of the estimation of exhaust emissions using the Vehicle Specific Power model. For the aggregated estimation of travel emissions, we use the aggregated traffic dynamics based on the Macroscopic Fundamental Diagram dynamics and COPERT V emission model. Our results show that the aggregated methodology underestimates CO2 emissions by 30% and NOx emissions by 32%, in agreement with the existing literature. Despite the observed discrepancies between the estimated emissions, the aggregated traffic dynamics approach based on the Macroscopic Fundamental Diagram is computationally lighter than a microscopic one, and therefore more appropriate for large-scale applications.