Automated material handling systems in semiconductor fabs are operated by a material control system (MCS) that must schedule a relay route for every transport command online, before execution. This is a data-driven scheduling problem in which route cost is dominated in the upper tail by queueing at heterogeneous, partially observable relay equipment, so route selection requires estimating both delivery time and congestion risk at the decision moment. This paper proposes a transport-network-aware dynamic congestion representation (TN-DCR). Built on a static directed transport graph induced by historically observed relay segments, TN-DCR combines structural route priors, multi-window network-wide congestion context, route-level bottleneck exposure, and an inductive graph-aware route embedding, all constructed under a prediction-time-safety invariant that admits only information observed strictly before the prediction moment. The representation feeds separate queue- and transfer-time regressors and an ordinal multi-label classifier producing calibrated multi-threshold exceedance scores, with an empirical-Bayes stock-key residual correction reducing systematic queue-time underprediction. The predictions serve as costs in a risk-constrained route-scheduling rule that minimizes predicted delivery time subject to a bound on extreme-congestion probability, embedding the learned predictors within a lightweight operations-research decision model. In a controlled closed-loop evaluation, mean delivery time falls by 16.4\% and internal resource waiting time by 22.6\% while throughput remains essentially unchanged.

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