### 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)

current_options = &p_options;
	Variant ret;
	GDVIRTUAL_CALL(_get_internal_option_update_view_required, p_category, p_option, ret);
	current_options = nullptr;
	return ret;
}
void EditorScenePostImportPlugin::internal_process(InternalImportCategory p_category, Node *p_base_scene, Node *p_node, Ref<Resource> p_resource, const Dictionary &p_options) {
	current_options_dict = &p_options;
	GDVIRTUAL_CALL(_internal_process, p_category, p_base_scene, p_node, p_resource);
	current_options_dict = nullptr;
}
void EditorScenePostImportPlugin::get_import_options(const String &p_path, List<ResourceImporter::ImportOption> *r_options) {
	current_option_list = r_options;
	GDVIRTUAL_CALL(_get_import_options, p_path);
	current_option_list = nullptr;
}
Variant EditorScenePostImportPlugin::get_option_visibility(const String &p_path, bool p_for_animation, const String &p_option, const HashMap<StringName, Variant> &p_options) const {
	current_options = &p_options;
	Variant ret;
	GDVIRTUAL_CALL(_get_option_visibility, p_path, p_for_animation, p_option, ret);
	current_options = nullptr;
	return ret;
}
void EditorScenePostImportPlugin::pre_process(Node *p_scene, const HashMap<StringName, Variant> &p_options) {
	current_options = &p_options;
	GDVIRTUAL_CALL(_pre_process, p_scene);
	current_options = nullptr;
}
void EditorScenePostImportPlugin::post_process(Node *p_scene, const HashMap<StringName, Variant> &p_options) {