Oh! I just remembered that you might need to set:
“alphaMode”: “BLEND”
``
on the material. This is something the exporter should be doing for transparent materials, or giving you a way to choose which materials are transparent. I know the glTF exporter in Blender can do this:
https://docs.blender.org/manual/en/dev/addons/io_gltf2.html#blend-modes
If you need to set this manually in the glTF, this sample model is a good example:
This line specifically: