### 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)

}
			external_paths->set_title(TTR("Set paths to save meshes as resource files on Reimport"));
			external_paths->set_ok_button_text(TTR("Set Paths"));
		} break;
		case ACTION_CHOOSE_ANIMATION_SAVE_PATHS: {
			for (const KeyValue<String, AnimationData> &E : animation_map) {
				AnimationData &ad = animation_map[E.key];
				TreeItem *item = external_path_tree->create_item(root);
				String name = ad.scene_node->get_text(0);
				item->set_cell_mode(0, TreeItem::CELL_MODE_CHECK);
				item->set_icon(0, get_theme_icon(SNAME("Animation"), SNAME("EditorIcons")));
				item->set_text(0, name);
				if (ad.settings.has("save_to_file/enabled") && bool(ad.settings["save_to_file/enabled"])) {
					item->set_text(2, "Already Saving");
					item->set_tooltip_text(2, TTR("This animation already saves to an external resource, no action will be taken."));
				} else {
					item->set_metadata(0, E.key);
					item->set_editable(0, true);
					item->set_checked(0, true);
					String path = p_path.path_join(name);
					if (external_extension_type->get_selected() == 0) {
						path += ".tres";
					} else {
						path += ".res";
					}
					item->set_text(1, path);
					if (FileAccess::exists(path)) {
						item->set_text(2, "Warning: File exists");
						item->set_tooltip_text(2, TTR("Existing file with the same name will be replaced on import."));
						item->set_icon(2, get_theme_icon(SNAME("StatusWarning"), SNAME("EditorIcons")));