Physics-informed deep learning (PIDL) neural networks have shown their capability as a useful instrument for transportation practitioners in utilizing the underlying relationship between the state variables for traffic state estimation (TSE). Another efficient traffic management approach is implementing varying speed limits (VSLs) on transportation corridors to control traffic and mitigate congestion. However, the existing training architecture of PIDL in the literature cannot accommodate the changing traffic characteristics on a freeway with VSL. To tackle this challenge, we propose a novel framework integrating teacher-student ensemble training with PIDL neural networks for TSE under VSL scenarios. The physics of flow conservation law is encoded locally in the teacher models by PIDL, and the student model uses a multi-layer perceptron classifier (MLP) to identify traffic characteristics and selects the ensemble member of PIDL neural networks for TSE. This integrated framework provides a natural solution for capturing the heterogeneity of VSL and accurately addressing the TSE problem. The case study results validate the proposed ensemble approach, demonstrating its superior performance in TSE compared to other popular baseline methods, as indicated by relative L2 error.