### 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)

r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "slice_" + itos(i + 1) + "/loop_mode", PROPERTY_HINT_ENUM, "None,Linear,Pingpong"), 0));
				r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "slice_" + itos(i + 1) + "/save_to_file/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
				r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "slice_" + itos(i + 1) + "/save_to_file/path", PROPERTY_HINT_SAVE_FILE, ".res,*.tres"), ""));
				r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "slice_" + itos(i + 1) + "/save_to_file/keep_custom_tracks"), false));
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE: {
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "import/skip_import", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "optimizer/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), true));
			r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "optimizer/max_velocity_error", PROPERTY_HINT_RANGE, "0,1,0.01"), 0.01));
			r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "optimizer/max_angular_error", PROPERTY_HINT_RANGE, "0,1,0.01"), 0.01));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "optimizer/max_precision_error", PROPERTY_HINT_NONE, "1,6,1"), 3));
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "compression/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "compression/page_size", PROPERTY_HINT_RANGE, "4,512,1,suffix:kb"), 8));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "import_tracks/position", PROPERTY_HINT_ENUM, "IfPresent,IfPresentForAll,Never"), 1));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "import_tracks/rotation", PROPERTY_HINT_ENUM, "IfPresent,IfPresentForAll,Never"), 1));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "import_tracks/scale", PROPERTY_HINT_ENUM, "IfPresent,IfPresentForAll,Never"), 1));
		} break;
		case INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE: {
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "import/skip_import", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::OBJECT, "retarget/bone_map", PROPERTY_HINT_RESOURCE_TYPE, "BoneMap", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), Variant()));
		} break;
		default: {
		}
	}
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		post_importer_plugins.write[i]->get_internal_import_options(EditorScenePostImportPlugin::InternalImportCategory(p_category), r_options);
	}
}
bool ResourceImporterScene::get_internal_option_visibility(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const {