LiDAR is a critical sensor for autonomous driving and robotics, yet it remains vulnerable to adverse conditions such as fog, rain, transparent objects, and low-reflectance surfaces. Full-waveform LiDAR (FWL) addresses these limitations by capturing the complete return waveform as a histogram, preserving rich reflection characteristics including multi-path echoes and weak signals. While recent Transformer-based approaches have demonstrated promise on FWL data, two fundamental bottlenecks remain: high computational cost from redundant tokens in low-intensity background regions, and limited generalization due to scarce annotated training data. We address both bottlenecks by exploiting the physical structure inherent to FWL data. First, we propose FWL-ToPM, a token pruning and merging mechanism that leverages intensity distributions to selectively reduce tokens while retaining critical waveform content. Second, we introduce FWLAug, a data augmentation framework designed as a regularization method that preserves waveform structure, retaining the Time-of-Flight waveform of each ray and the frustum geometry, to improve generalization to unseen scenes. Evaluated on the Ghost-FWL benchmark, FWL-ToPM achieves over 8 times speedup at real-time throughput alongside a nearly 9-point F1 gain over the prior state of the art, establishing the first real-time FWL Transformer that simultaneously improves accuracy. FWLAug further improves performance on both the standard benchmark and an out-of-distribution test set of unseen scenes. Together, these methods push FWL-based perception toward practical deployment. The code and the OOD dataset are publicly available and can be accessed via the project page: https://keio-csg.github.io/FWL-ToPM

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