Classifying VPN-encrypted traffic by application category typically relies on datasets that collect non-VPN and VPN traffic in separate sessions, conflating encapsulation effects with session-level differences in user behavior, timing, and application mix. We use a recently published WireGuard tunnel dataset in which pre- and post-tunnel traffic is captured simultaneously, with a packet-level match ratio above 99.9%. This matched-capture design eliminates session-level confounds and enables a cross-domain benchmark: models are trained on non-VPN flows and tested on the VPN view of the same underlying flows. We compare whole-flow statistical aggregates (FlowFeatures) and Sequence of Packet Length and Time (SPLT) early-flow fingerprints across Random Forest, XGBoost, and a multi-scale CNN1D. Cross-domain transfer depends jointly on representation and model: tree ensembles achieve balanced accuracy of 0.84-0.93 with FlowFeatures but only 0.60-0.75 with flattened SPLT, whereas CNN1D processes the same SPLT fingerprint as a sequence and achieves the strongest transfer overall (balanced accuracy 0.98, macro F1 0.89) without any VPN data during training.

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