### 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)

TRACK_CHANNEL_POSITION,
		TRACK_CHANNEL_ROTATION,
		TRACK_CHANNEL_SCALE,
		TRACK_CHANNEL_BLEND_SHAPE,
		TRACK_CHANNEL_MAX
	};
	void _optimize_track_usage(AnimationPlayer *p_player, AnimationImportTracks *p_track_actions);
	bool animation_importer = false;
public:
	static ResourceImporterScene *get_scene_singleton() { return scene_singleton; }
	static ResourceImporterScene *get_animation_singleton() { return animation_singleton; }
	static void add_post_importer_plugin(const Ref<EditorScenePostImportPlugin> &p_plugin, bool p_first_priority = false);
	static void remove_post_importer_plugin(const Ref<EditorScenePostImportPlugin> &p_plugin);
	const Vector<Ref<EditorSceneFormatImporter>> &get_importers() const { return importers; }
	static void add_importer(Ref<EditorSceneFormatImporter> p_importer, bool p_first_priority = false);
	static void remove_importer(Ref<EditorSceneFormatImporter> p_importer);
	static void clean_up_importer_plugins();
	virtual String get_importer_name() const override;
	virtual String get_visible_name() const override;
	virtual void get_recognized_extensions(List<String> *p_extensions) const override;
	virtual String get_save_extension() const override;
	virtual String get_resource_type() const override;
	virtual int get_format_version() const override;
	virtual int get_preset_count() const override;
	virtual String get_preset_name(int p_idx) const override;
	enum InternalImportCategory {