### 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_path_tree->clear();
	TreeItem *root = external_path_tree->create_item();
	save_path_items.clear();
	switch (current_action) {
		case ACTION_EXTRACT_MATERIALS: {
			for (const KeyValue<String, MaterialData> &E : material_map) {
				MaterialData &md = material_map[E.key];
				TreeItem *item = external_path_tree->create_item(root);
				String name = md.material_node->get_text(0);
				item->set_cell_mode(0, TreeItem::CELL_MODE_CHECK);
				item->set_icon(0, get_theme_icon(SNAME("StandardMaterial3D"), SNAME("EditorIcons")));
				item->set_text(0, name);
				if (md.has_import_id) {
					if (md.settings.has("use_external/enabled") && bool(md.settings["use_external/enabled"])) {
						item->set_text(2, "Already External");
						item->set_tooltip_text(2, TTR("This material already references an external file, no action will be taken.\nDisable the external property for it to be extracted again."));
					} 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";
						}