We quantify decoder dependence in surface-code threshold studies under two matched regimes: Pauli noise and native GKP-style Gaussian displacement digitization. Using LiDMaS+ v1.1.0, we benchmark MWPM, Union-Find (UF), Belief Propagation (BP), and neural-guided MWPM with fixed seeds, identical sweep grids, and unified reporting across runs 06--14. At $d=5$ and $σ=0.20$, MWPM and UF define the Pareto frontier, with (runtime, LER) = (1.341 s, 0.2273) and (1.332 s, 0.2303); neural-guided MWPM is slower and less accurate (1.396 s, 0.3730), and BP is dominated (7.640 s, 0.6107). Crossing-bootstrap diagnostics are stable only for MWPM, with median $σ^\star_{3,5}=0.10$ (1911/2000 valid) and $σ^\star_{5,7}=0.1375$ (1941/2000 valid), while other decoders show no valid crossing samples. Dense-window scanning over $σ\in [0.08,0.24]$ returns NaN crossings for all decoders, confirming estimator- and window-sensitive threshold localization. Rank-stability and effect-size bootstrap analyses reinforce ordering robustness: BP remains rank 4, neural-guided MWPM rank 3, and MWPM-UF differences are small ($Δ_{\mathrm{MWPM-UF}}=-0.00383$, 95\% interval $[-0.0104,0.00329]$) across $σ\in [0.05,0.35]$. Threaded execution preserves statistical fidelity while improving throughput: $1.34\times$ speedup in Pauli mode and $1.94\times$ in native GKP mode, with mean $|Δ\mathrm{LER}|$ $6.07\times10^{-3}$ and $5.20\times10^{-3}$, respectively. We therefore recommend estimator-conditional threshold reporting coupled to runtime-fidelity checks for reproducible hardware-facing practical future decoder benchmarking workflows.