The present article adequately supports a twofold objective. On one hand, the study of the dynamic mechanical behavior of polypropylene/polyamide-6 blends modified by a novel compatibilizer was the objective. This was previously obtained by chemical modification of an atactic polypropylene polymerization waste. On the other hand, the accurate predictions of these properties in the experimental space scanned was the objective. As a novelty, this compatibilizer contains grafts rather than just maleated ones. Therefore, it consists precisely of an atactic polymer containing succinic anhydride (SA) bridges and both backbone and terminal grafted succinyl-fluorescein groups (SFSA) attached to the atactic backbone (aPP-SFSA). Therefore, it contains 6.2% of total grafting (2.5% as SA and 3.7% as SF), which is equivalent to 6.2 × 10−4 g·mol−1. This interfacial agent was uniquely designed and obtained by the authors themselves. Essentially, this article focuses on how the beneficial effect of both PA6 and aPP-SFSA varies the elastic (E’) and the viscous (E’’) behavior of the iPP/aPP-SFSA/PA6 blend at the iPP glass transition. Thus, we accurately measured the Dynamic Mechanical Analysis (DMA) parameters (E’, E’’) at this specific point considering it represents an extremely unfavorable scenario for the interfacial modifier due to mobility restrictions. Hence, this evidences the real interfacial modifications caused by aPP-SFSA to the iPP/PA6 system. Even more, and since each of the necessary components in the blend typically interacts with one another, we employed a Box–Wilson experimental design by its marked resemblance to the “agent-based models”. In this manner, we obtained complex algorithms accurately forecasting the dynamic mechanical behavior of the blends for all the composition range of the iPP/aPP-SFSA/PA6 system at the glass transition of iPP.