GLTF/GLB Export in ThreeJS: Disrupting Scene Hierarchy

I am exporting my scene using a very basic approach:

function save(blob, filename) {
  const link = document.createElement("a");
  link.href = URL.createObjectURL(blob);
  link.download = filename;
  link.click();
  URL.revokeObjectURL(link);
}

function saveString(text, filename) {
  save(new Blob([text], { type: "text/plain" }), filename);
}

function saveArrayBuffer(buffer, filename) {
  save(new Blob([buffer], { type: "application/octet-stream" }), filename);
}

const exporter = new GLTFExporter();
exporter.parse(
  scene,
  function (result) {
    const name = `${modelName}.glb`;
    if (result instanceof ArrayBuffer) {
      saveArrayBuffer(result, name);
    } else {
      const output = JSON.stringify(result, null, 2);
      saveString(output, name);
    }
  },
  function (error) {
    console.log(error);
  },
  {
    binary: true,
    animations: [mixer.clipAction(model.animations[0]).getClip()],
  }
);

But as can be understood from the title, the hierarchy in my scene is being disrupted. Typically, my objects are directly placed under the scene. However, during the export process, a new empty object is created, and all my objects are nested within it. I desire to maintain the original structure of my scene.

before

after

note: my scene contains animations that belong to objects.

Because glTF is not a three.js-specific format, its structures (nodes, meshes, primitives, ...) are not 1:1 analogs of three.js structures (Scene, Group, Object3D, Mesh, ...). three.js does the conversion in one direction during loading, and in another direction during export, with the goal of preserving the visual correctness of the scene.

Unfortunately, as you've found here, there's no guarantee that the round-trip will reproduce the exact underlying structure of the original three.js scene. There are some other related implications – texture are recompressed, and might lose a little quality.

There might be other ways to go about this, depending on what you're ultimately trying to do, but that might be better suited for a forum discussion than a Stack Overflow Q/A.