We are using a custom glTF pipeline to render pointclouds (not even babylonjs) but use the babylonjs sandbox to crosscheck and it has been an absolutely invaluable tool so far . Suddenly (as in last month or so it was still working?!) it seems that something broke in babylonjs.
This is how babylonjs renders my testfile when LOD is activated. Note that I activated the camera that came from the glTF file. Also I increased the point size in the standard material to see something. I have hidden all LODs to make sure that it is really showing the base asset only.
The red cone is placed left of the blue cone.
Now reloading the same file after disabling the MSFT_lod extension (again point size increased and glTF cam activated) I see the expected result. (Screenshot in a reply as I am only allowed to upload one image :D)
The glTF file: aa-babylonjs-test.gltf · GitHub