### 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)

update_view_timer->start();
}
void SceneImportSettings::open_settings(const String &p_path, bool p_for_animation) {
	if (scene) {
		memdelete(scene);
		scene = nullptr;
	}
	editing_animation = p_for_animation;
	scene_import_settings_data->settings = nullptr;
	scene_import_settings_data->path = p_path;
	
	data_mode->set_tab_hidden(1, p_for_animation);
	data_mode->set_tab_hidden(2, p_for_animation);
	action_menu->get_popup()->set_item_disabled(action_menu->get_popup()->get_item_id(ACTION_EXTRACT_MATERIALS), p_for_animation);
	action_menu->get_popup()->set_item_disabled(action_menu->get_popup()->get_item_id(ACTION_CHOOSE_MESH_SAVE_PATHS), p_for_animation);
	base_path = p_path;
	material_set.clear();
	mesh_set.clear();
	animation_map.clear();
	material_map.clear();
	mesh_map.clear();
	node_map.clear();