Key phenotypic traits, such as crop size, volume, and weight, can be estimated non-destructively from point clouds. In practice, however, point clouds of crops are typically incomplete due to self-occlusion, leading to systematic errors when estimating these traits. To overcome this limitation, crop traits can be inferred directly from incomplete point clouds using deep learning-based regression networks. These networks, however, may perform suboptimally, because their predictions do not incorporate prior geometric knowledge of the crop. Such geometric knowledge is often available in structured settings, such as on a potato harvester, where the fixed distance between the camera and the conveyor belt allows tuber height to be derived from the point cloud. To exploit this geometric cue, we introduce PointRAFT, a high-throughput point cloud regression network that incorporates object height through a dedicated height embedding. We hypothesized that this height embedding improves tuber weight estimation from partial point clouds. To test this hypothesis, we collected 26,688 point clouds of 859 potato tubers on an operational harvester, spanning four cultivars and three growing seasons. On a test set of 5,254 point clouds representing 172 tubers, PointRAFT achieved a mean absolute error (MAE) of 11.7 g and a root mean squared error (RMSE) of 17.1 g, outperforming six point cloud regression networks without a height embedding. Requiring only 6.3 ms per point cloud for preprocessing and inference, PointRAFT is fast enough for high-throughput weight estimation on a commercial potato harvester. Beyond potato weight estimation, PointRAFT provides a versatile regression network applicable to a wide range of 3D phenotyping and robotic perception tasks. The code, network weights, and a subset of the dataset are publicly available at https://github.com/pieterblok/pointraft.

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