Repository: godot
Issue: EditorSceneFormatImport only adds the top-level node to scenes
Labels: topic:editor,documentation,topic:import,topic:3d

### Godot version

4.0.3-stable, 4.1.dev3.official (a67d37f7c)

### System information

OS: Pop!_OS 20.04 LTS
Godot Version: 4.0.3-stable, 4.1.dev3.official (a67d37f7c)
Rendering Driver: Vulkan
Rendering Method: Forward+
Graphics Card: nvidia geforce GTX 1070

### Issue description

Custom 3d model imported via a `EditorSceneFormatImport` plugin does not retain child nodes.

## Observed Behavior
The `_import_scene()` method of my `EditorSceneFormatImport` plugin creates and returns a `Node3D` with several child nodes, including a `MeshInstance3D`, `Skeleton3D`, and `AnimationPlayer`. I can tell that the model loaded correctly, because when I open the advanced import pane, it shows the full hierarchy.
![blue_advanced_import](https://github.com/godotengine/godot/assets/44122378/3437ef1e-6cfb-4b29-961b-69098b33d7ae)

However, only the top-level node is present when this object gets added to the scene tree. Thus, because the top-level node is just a `Node3D`, nothing is visible either in the scene, or when I open the model as a scene on its own.

In the below scene
- `child_blue` should be a blue triangle with skeleton and animation, but none of those are present
- `root_red` shows that if the importer only returns the `MeshInstance3D`, but none of the rest of the hierarchy (skeleton, animations, etc), then it is visible
- `RiggedSimple` is an example `glb` file from [Khronos](https://github.com/KhronosGroup/glTF-Sample-Models/tree/master/2.0/RiggedSimple) 
![blue_in_scene](https://github.com/godotengine/godot/assets/44122378/351e4188-8177-4148-8622-80259a19295f)
![node_open_as_scene](https://github.com/godotengine/godot/assets/44122378/612b2d98-e303-4cd8-9102-6ab9185f3d80)


If I do not build the whole hierarchy in the `_import_scene()`, but rather simply return a `MeshInstance3D`, it is visible in scenes, but has lost all skeleton / animation info.
![red_advanced_import](https://github.com/godotengine/godot/assets/44122378/95bb7e0d-6132-491b-9972-9635bae6065f)

This behavior can be seen in `demo_editor_import.tscn`

## Expected Behavior
I would expect the full node hierarchy to show up in the scene, similar to what happens when I import a `gltf` model.
![gltf_open_as_scene](https://github.com/godotengine/godot/assets/44122378/f1744c56-d96f-4628-9f88-6c1eb529c17e)

## Additional Notes
If I call my model parsing script directly via `gdscript`, rather than through the import plugin, the model gets added to the scene exactly like I expect. This can be seen in `demo_import_from_script.tscn`. It still doesn't work if I use `load()` or `preload()`, only if I manually call `preload("res://addons/importer/model_importer.gd").load_file("res://models/child_blue.model")`

### Steps to reproduce

1) Create an `EditorSceneFormatImport` script
2) In `_import_scene()` from that script, construct a scene consisting of `Node3D`s with child `Node3D`s
3) Drag an imported model from the `FileSystem` pane into a 3D scene
4) You should notice that only the top-level node is imported

### Minimal reproduction project

Minimal project is a git repo with two branches
- `main` has the example for `4.0.3`
- `4.1` has the example for `4.1` (though there are no important differences between it at `main`)

[minimal_editor_scene_format_import.zip](https://github.com/godotengine/godot/files/11583074/minimal_editor_scene_format_import.zip)