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Using the resultant profiles from 3D hydrodynamic simulations of relativistic jets interacting with neutron star merger wind ejecta, we show how the inhomogeneity of energy and velocity {across the jet surface profile} can alter the observed afterglow lightcurve. We find that the peak afterglow flux depends sensitively on the observer's line-of-sight, not only via the jet inclination but also through the jet rotation: for an observer viewing the afterglow within the GRB-bright jet core, we find a peak flux variability on the order $<0.5$ dex through rotational orientation and $<1.3$ dex for the polar inclination. An observed afterglow's peak flux can be used to infer the jet kinetic energy, and where a top-hat jet is assumed, we find the range of inferred jet kinetic energies for our various model afterglow lightcurves (with fixed model parameters), covers $\sim 1/3$ of the observed short GRB population. Additionally, we present an analytic jet structure function that includes physically motivated parameter uncertainties due to variability through the rotation of the source. % An approximation for the change in collimation due to the merger ejecta mass is included and we show that by considering the observed range of merger ejecta masses from short GRB kilonova candidates, a population of merger jets with a fixed intrinsic jet energy is capable of explaining the observed broad diversity seen in short GRB afterglows.