Results from the Stage I analysis enabled us to narrow down the potential design space to the best-performing configurations: single-stage ambient-temperature systems with passive biogas collection and a short HRT (≤ 5 days). These designs were further examined through uncertainty and sensitivity analyses, with bead size and bead lifetime varied within narrower ranges to exclude unlikely values based on published data. To have a more representative characterization of the performance and sustainability of the systems, a series of parameters in the process model was included to account for the technological uncertainties associated with stems from two key factors: (i) packed bed systems maintained over 74.3% COD removal for 95% of the simulated samples while the COD removal of fluidized bed systems was subject to much higher uncertainty; and (ii) 55-65% of a packed bed reactor's volume is filled with beads (compared to 3-25% for a fluidized bed reactor) and, as a result, the change in HRT leads to greater changes in packed bed reactor size and the amount encapsulant material needed (the latter of which is the dominant contributor to its cost and impacts). Although pair-wise comparison showed a packed bed system always outperformed a fluidized bed system at rCOD under identical conditions, the significant sensitivity of LC and CI to HRT (𝐷 ∈ [0.87, 0.98], 𝑝 < 0.0001;