### 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)

INTERNAL_IMPORT_CATEGORY_NODE = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_NODE,
		INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE,
		INTERNAL_IMPORT_CATEGORY_MESH = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MESH,
		INTERNAL_IMPORT_CATEGORY_MATERIAL = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MATERIAL,
		INTERNAL_IMPORT_CATEGORY_ANIMATION = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_ANIMATION,
		INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE,
		INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE,
		INTERNAL_IMPORT_CATEGORY_MAX = EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MAX
	};
	void get_internal_import_options(InternalImportCategory p_category, List<ImportOption> *r_options) const;
	bool get_internal_option_visibility(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const;
	bool get_internal_option_update_view_required(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const;
	virtual void get_import_options(const String &p_path, List<ImportOption> *r_options, int p_preset = 0) const override;
	virtual bool get_option_visibility(const String &p_path, const String &p_option, const HashMap<StringName, Variant> &p_options) const override;
	
	virtual int get_import_order() const override { return ResourceImporter::IMPORT_ORDER_SCENE; }