### 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)

{
		mesh_preview = memnew(MeshInstance3D);
		base_viewport->add_child(mesh_preview);
		mesh_preview->hide();
		material_preview.instantiate();
	}
	{
		collider_mat.instantiate();
		collider_mat->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
		collider_mat->set_albedo(Color(0.5, 0.5, 1.0));
	}
	inspector = memnew(EditorInspector);
	inspector->set_custom_minimum_size(Size2(300 * EDSCALE, 0));
	inspector->set_property_name_style(EditorPropertyNameProcessor::get_settings_style());
	property_split->add_child(inspector);
	scene_import_settings_data = memnew(SceneImportSettingsData);
	set_ok_button_text(TTR("Reimport"));
	set_cancel_button_text(TTR("Close"));
	external_paths = memnew(ConfirmationDialog);
	add_child(external_paths);
	external_path_tree = memnew(Tree);
	external_paths->add_child(external_path_tree);
	external_path_tree->connect("button_clicked", callable_mp(this, &SceneImportSettings::_browse_save_callback));
	external_paths->connect("confirmed", callable_mp(this, &SceneImportSettings::_save_dir_confirm));
	external_path_tree->set_columns(3);
	external_path_tree->set_column_titles_visible(true);
	external_path_tree->set_column_expand(0, true);
	external_path_tree->set_column_custom_minimum_width(0, 100 * EDSCALE);
	external_path_tree->set_column_title(0, TTR("Resource"));
	external_path_tree->set_column_expand(1, true);