### 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)

class AnimationPlayer;
class ImporterMesh;
class EditorSceneFormatImporter : public RefCounted {
	GDCLASS(EditorSceneFormatImporter, RefCounted);
protected:
	static void _bind_methods();
	Node *import_scene_wrapper(const String &p_path, uint32_t p_flags, Dictionary p_options);
	Ref<Animation> import_animation_wrapper(const String &p_path, uint32_t p_flags, Dictionary p_options);
	GDVIRTUAL0RC(int, _get_import_flags)
	GDVIRTUAL0RC(Vector<String>, _get_extensions)
	GDVIRTUAL3R(Object *, _import_scene, String, uint32_t, Dictionary)
	GDVIRTUAL1(_get_import_options, String)
	GDVIRTUAL3RC(Variant, _get_option_visibility, String, bool, String)
public:
	enum ImportFlags {
		IMPORT_SCENE = 1,
		IMPORT_ANIMATION = 2,
		IMPORT_FAIL_ON_MISSING_DEPENDENCIES = 4,
		IMPORT_GENERATE_TANGENT_ARRAYS = 8,
		IMPORT_USE_NAMED_SKIN_BINDS = 16,
		IMPORT_DISCARD_MESHES_AND_MATERIALS = 32, 
	};
	virtual uint32_t get_import_flags() const;
	virtual void get_extensions(List<String> *r_extensions) const;
	virtual Node *import_scene(const String &p_path, uint32_t p_flags, const HashMap<StringName, Variant> &p_options, List<String> *r_missing_deps, Error *r_err = nullptr);
	virtual void get_import_options(const String &p_path, List<ResourceImporter::ImportOption> *r_options);
	virtual Variant get_option_visibility(const String &p_path, bool p_for_animation, const String &p_option, const HashMap<StringName, Variant> &p_options);
	EditorSceneFormatImporter() {}
};
class EditorScenePostImport : public RefCounted {