### 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)

mutable const HashMap<StringName, Variant> *current_options = nullptr;
	mutable const Dictionary *current_options_dict = nullptr;
	List<ResourceImporter::ImportOption> *current_option_list = nullptr;
	InternalImportCategory current_category = INTERNAL_IMPORT_CATEGORY_MAX;
protected:
	GDVIRTUAL1(_get_internal_import_options, int)
	GDVIRTUAL3RC(Variant, _get_internal_option_visibility, int, bool, String)
	GDVIRTUAL2RC(Variant, _get_internal_option_update_view_required, int, String)
	GDVIRTUAL4(_internal_process, int, Node *, Node *, Ref<Resource>)
	GDVIRTUAL1(_get_import_options, String)
	GDVIRTUAL3RC(Variant, _get_option_visibility, String, bool, String)
	GDVIRTUAL1(_pre_process, Node *)
	GDVIRTUAL1(_post_process, Node *)
	static void _bind_methods();
public:
	Variant get_option_value(const StringName &p_name) const;
	void add_import_option(const String &p_name, Variant p_default_value);
	void add_import_option_advanced(Variant::Type p_type, const String &p_name, Variant p_default_value, PropertyHint p_hint = PROPERTY_HINT_NONE, const String &p_hint_string = String(), int p_usage_flags = PROPERTY_USAGE_DEFAULT);
	virtual void get_internal_import_options(InternalImportCategory p_category, List<ResourceImporter::ImportOption> *r_options);
	virtual Variant get_internal_option_visibility(InternalImportCategory p_category, bool p_for_animation, const String &p_option, const HashMap<StringName, Variant> &p_options) const;
	virtual Variant get_internal_option_update_view_required(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const;
	virtual void internal_process(InternalImportCategory p_category, Node *p_base_scene, Node *p_node, Ref<Resource> p_resource, const Dictionary &p_options);
	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) const;
	virtual void pre_process(Node *p_scene, const HashMap<StringName, Variant> &p_options);
	virtual void post_process(Node *p_scene, const HashMap<StringName, Variant> &p_options);
	EditorScenePostImportPlugin() {}
};
VARIANT_ENUM_CAST(EditorScenePostImportPlugin::InternalImportCategory)
class ResourceImporterScene : public ResourceImporter {