### 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_tree->ensure_cursor_is_visible();
		}
		if (p_from != scene_tree) {
			md.scene_node->uncollapse_tree();
			md.scene_node->select(0);
			scene_tree->ensure_cursor_is_visible();
		}
		if (p_from != material_tree) {
			md.material_node->uncollapse_tree();
			md.material_node->select(0);
			material_tree->ensure_cursor_is_visible();
		}
		scene_import_settings_data->settings = &md.settings;
		scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MATERIAL;
	}
	selected_type = p_type;
	selected_id = p_id;
	selecting = false;
	_update_camera();
	List<ResourceImporter::ImportOption> options;
	if (editing_animation) {
		if (scene_import_settings_data->category == ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX) {
			ResourceImporterScene::get_animation_singleton()->get_import_options(base_path, &options);
		} else {
			ResourceImporterScene::get_animation_singleton()->get_internal_import_options(scene_import_settings_data->category, &options);
		}
	} else {
		if (scene_import_settings_data->category == ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX) {
			ResourceImporterScene::get_scene_singleton()->get_import_options(base_path, &options);
		} else {