### 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)

GDVIRTUAL_CALL(_get_import_options, p_path);
}
Variant EditorSceneFormatImporter::get_option_visibility(const String &p_path, bool p_for_animation, const String &p_option, const HashMap<StringName, Variant> &p_options) {
	Variant ret;
	GDVIRTUAL_CALL(_get_option_visibility, p_path, p_for_animation, p_option, ret);
	return ret;
}
void EditorSceneFormatImporter::_bind_methods() {
	GDVIRTUAL_BIND(_get_import_flags);
	GDVIRTUAL_BIND(_get_extensions);
	GDVIRTUAL_BIND(_import_scene, "path", "flags", "options");
	GDVIRTUAL_BIND(_get_import_options, "path");
	GDVIRTUAL_BIND(_get_option_visibility, "path", "for_animation", "option");
	BIND_CONSTANT(IMPORT_SCENE);
	BIND_CONSTANT(IMPORT_ANIMATION);
	BIND_CONSTANT(IMPORT_FAIL_ON_MISSING_DEPENDENCIES);
	BIND_CONSTANT(IMPORT_GENERATE_TANGENT_ARRAYS);
	BIND_CONSTANT(IMPORT_USE_NAMED_SKIN_BINDS);
	BIND_CONSTANT(IMPORT_DISCARD_MESHES_AND_MATERIALS);
}
void EditorScenePostImport::_bind_methods() {
	GDVIRTUAL_BIND(_post_import, "scene")
	ClassDB::bind_method(D_METHOD("get_source_file"), &EditorScenePostImport::get_source_file);
}
Node *EditorScenePostImport::post_import(Node *p_scene) {