Point transformer traning crashes if shape is not [n, 16]

### Checklist

- [x] I have searched for [similar issues](https://github.com/isl-org/Open3D-ML/issues).
- [x] I have tested with the [latest development wheel](http://www.open3d.org/docs/latest/getting_started.html#development-version-pip).
- [x] I have checked the [release documentation](http://www.open3d.org/docs/release/) and the [latest documentation](http://www.open3d.org/docs/latest/) (for `main` branch).

### Describe the issue

I have been trying to train my custom dataset on point transformer using torch pipeline but training crashes due less number of neighbours.

### Steps to reproduce the bug

```python
part of config with many number of points:
train_dir: train
val_dir: [val, test]
test_dir: []
dataset_info: dataset_info.json
sampler:
name: SemSegRandomSampler
test_result_folder: ./test
min_points: 32768
padding_noise_std: 0.01
```

### Error message

@pop-os:~/Documents/HPC pipeline$ python training_pipeline/open3dml-clone/scripts/run_pipeline.py torch \
-c training_pipeline/configs/pointtransformer_helios.yml \
--dataset.dataset_path data_processing/helios_open3dml_data \
--pipeline SemanticSegmentation \
--dataset.use_cache True \
--device cuda \
--pipeline.log_level DEBUG
Using external Open3D-ML in /homeHPC pipeline/training_pipeline/open3dml-clone
regular arguments
backend: gloo
batch_size: null
cfg_dataset: null
cfg_file: training_pipeline/configs/pointtransformer_helios.yml
cfg_model: null
cfg_pipeline: null
ckpt_path: null
dataset: null
dataset_path: null
device: cuda
device_ids:
- '0'
framework: torch
host: localhost
main_log_dir: null
max_epochs: null
mode: null
model: null
node_rank: 0
nodes: 1
pipeline: SemanticSegmentation
port: '12355'
seed: 0
split: train

extra arguments
dataset.dataset_path: data_processing/helios_open3dml_data
dataset.use_cache: 'True'
pipeline.log_level: DEBUG

INFO - 2025-09-26 14:34:01,560 - heliosconstruction - HeliosConstruction dataset initialized with 152 train / 48 val / 0 test files.
INFO - 2025-09-26 14:34:01,703 - semantic_segmentation - DEVICE : cuda
INFO - 2025-09-26 14:34:01,703 - semantic_segmentation - Logging in file : ./logs/PointTransformer_HeliosConstruction_torch/log_train_2025-09-26_14-34-01.txt
INFO - 2025-09-26 14:34:01,704 - heliosconstruction - Found 152 point clouds for train
INFO - 2025-09-26 14:34:01,705 - heliosconstruction - Found 48 point clouds for validation
INFO - 2025-09-26 14:34:01,956 - semantic_segmentation - Initializing from scratch.
INFO - 2025-09-26 14:34:01,957 - semantic_segmentation - Writing summary in train_log/00020_PointTransformer_HeliosConstruction_torch.
INFO - 2025-09-26 14:34:01,957 - semantic_segmentation - Started training
INFO - 2025-09-26 14:34:01,957 - semantic_segmentation - === EPOCH 0/200 ===
training: 0%| | 0/76 [00:00
sys.exit(main())
^^^^^^
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/scripts/run_pipeline.py", line 192, in main
pipeline.run_train()
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/pipelines/semantic_segmentation.py", line 416, in run_train
results = model(inputs['data'])
^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home//Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/models/point_transformer.py", line 175, in forward
p, f, r = self.encoders[i]([points[i], feats[i], row_splits[i]])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/container.py", line 217, in forward
input = module(input)
^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/models/point_transformer.py", line 643, in forward
feat = self.relu(self.bn2(self.transformer2([point, feat, row_splits])))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda3/envs/Helios/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/models/point_transformer.py", line 430, in forward
feat_k = queryandgroup(self.nsample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/models/point_transformer.py", line 680, in queryandgroup
idx = knn_batch(points,
^^^^^^^^^^^^^^^^^
File "/home/Documents/HPC pipeline/training_pipeline/open3dml-clone/ml3d/torch/models/point_transformer.py", line 734, in knn_batch
return ans.neighbors_index.reshape(-1, k).long().cuda()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: shape '[-1, 16]' is invalid for input of size 345

### Expected behavior

_No response_

### Open3D, Python and System information

```markdown
- Operating system: Ubuntu 22.04,
- Python version: Python 3.11
- Open3D version: 0.18.0
- System type:
- Is this remote workstation?: no
- How did you install Open3D?: pip
- Compiler version (if built from source):
```

### Additional information

The crash comes from knn_search in the current Open3D release returning ragged neighbor lists—some queries yield fewer than 16 neighbours, so Open3D-ML’s
PointTransformer (which assumes a fixed k) can’t reshape the tensor. That behaviour changed in Open3D ≥0.18; the upstream Open3D-ML master hasn’t patched this branch
yet,