### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

}
	{
		
		node_settings = node_settings.duplicate(true);
		
		List<ImportOption> iopts;
		if (Object::cast_to<ImporterMeshInstance3D>(p_node)) {
			get_internal_import_options(INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE, &iopts);
		} else if (Object::cast_to<AnimationPlayer>(p_node)) {
			get_internal_import_options(INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE, &iopts);
		} else if (Object::cast_to<Skeleton3D>(p_node)) {
			get_internal_import_options(INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE, &iopts);
		} else {
			get_internal_import_options(INTERNAL_IMPORT_CATEGORY_NODE, &iopts);
		}
		for (const ImportOption &E : iopts) {
			if (!node_settings.has(E.option.name)) {
				node_settings[E.option.name] = E.default_value;
			}
		}
	}
	{
		ObjectID node_id = p_node->get_instance_id();
		for (int i = 0; i < post_importer_plugins.size(); i++) {
			post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_NODE, p_root, p_node, Ref<Resource>(), node_settings);
			if (ObjectDB::get_instance(node_id) == nullptr) { 
				break;
			}
		}
	}