Analysis of aircraft observations of atmospheric trace gases is key towards improving our understanding of fundamental chemical processes and quantifying anthropogenic emissions. A common approach for such analysis is use of chemical transport models to produce 4-D fields for comparison with these observations together with various inversion techniques to constrain the underlying fluxes and chemistry. Yet, time and monetary constraints of expensive computational jobs for chemical transport modelling can be a significant hindrance. Here, we show the advantages of using potential temperature as a dynamical coordinate to compare such simulations to aircraft observations of trace gases whose concentration fields are strongly influenced by synoptic-scale transport. We use global observations of ethane and propane from the Atmospheric Tomography (ATom) aircraft mission and simulate global mole fractions for these gases using GEOS-Chem High Performance v13.4.1. We show, using potential temperature as an analysis coordinate, that Bayesian estimates of the fluxes of these gases in the Northern Hemisphere are largely invariant (± 10 %) even as the simulation spatial resolution is increased 100-fold. Our approach can have broad applications for the modelling of trace gases in the extra-tropics, particularly those with lifetimes long compared to synoptic timescales.