Special Economic Zones (SEZs) are widely promoted as catalysts for industrialization and export growth in developing countries, yet their capacity to generate sustainable and inclusive regional development remains debated, particularly in sub-Saharan Africa. This study investigates the impact of the Nkok SEZ in Gabon on the forestry sector—a novel case study—by analyzing the resulting economic and spatial disparities between the SEZ (homogeneous space) and its periphery (heterogeneous space). Combining robust econometric methods (Bias-Corrected Fixed Effects, OLS) and principal component analysis (PCA) on time-series data (2014–2022), we show that while the SEZ has significantly boosted export revenues (84%–97% growth) and industrial production through agglomeration and scale economies, these benefits remain largely concentrated. The periphery experiences weaker growth, reinforcing center-periphery dependencies and extractive specialization. Export revenues from the homogeneous space exhibit strong autoregressive effects (77%–94%) but limited macroeconomic diffusion (6%–25%), whereas the heterogeneous space shows lower autoregressive growth but a stronger historical influence on national aggregates, highlighting a structural polarization trap. To address these persistent imbalances, this paper introduces the SEMD model (Segmentation, Evaluation, and Multi-level Disparities Management). This operational framework proposes a six-fold territorial typology (from SEZs to informal circuits), hybrid quantitative-qualitative indicators, and proactive rebalancing mechanisms (vertical and horizontal channels) to institutionalize the diffusion of growth. The SEMD model offers a strategic tool for policymakers in the Global South to reconcile industrial performance with territorial cohesion, moving beyond the mere diagnosis of inequalities toward adaptive, real-time management of polarized development dynamics.