### 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)

defaults.clear();
	mesh_preview->hide();
	selected_id = "";
	selected_type = "";
	cam_rot_x = -Math_PI / 4;
	cam_rot_y = -Math_PI / 4;
	cam_zoom = 1;
	{
		base_subresource_settings.clear();
		Ref<ConfigFile> config;
		config.instantiate();
		Error err = config->load(p_path + ".import");
		if (err == OK) {
			List<String> keys;
			config->get_section_keys("params", &keys);
			for (const String &E : keys) {
				Variant value = config->get_value("params", E);
				if (E == "_subresources") {
					base_subresource_settings = value;
				} else {
					defaults[E] = value;
				}
			}
		}
	}
	scene = ResourceImporterScene::get_scene_singleton()->pre_import(p_path, defaults); 
	if (scene == nullptr) {
		EditorNode::get_singleton()->show_warning(TTR("Error opening scene"));
		return;
	}