We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO3) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.