### 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)

if (md.settings.has("save_to_file/enabled") && bool(md.settings["save_to_file/enabled"])) {
						item->set_text(2, "Already Saving");
						item->set_tooltip_text(2, TTR("This mesh 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")));
						} else {
							item->set_text(2, "Will save to new File");
							item->set_icon(2, get_theme_icon(SNAME("StatusSuccess"), SNAME("EditorIcons")));
						}
						item->add_button(1, get_theme_icon(SNAME("Folder"), SNAME("EditorIcons")));
					}
				} else {
					item->set_text(2, "No import ID");
					item->set_tooltip_text(2, TTR("Mesh has no name nor any other way to identify on re-import.\nPlease name it or ensure it is exported with an unique ID."));
					item->set_icon(2, get_theme_icon(SNAME("StatusError"), SNAME("EditorIcons")));
				}
				save_path_items.push_back(item);