### Godot version

4.0-rc6

### System information

Fedora 37, Mesa Intel ADL GT2

### Issue description

Code that works as expected at runtime fails with Nil references to (assigned) exported vars in the editor:

![tool_global_position_error](https://user-images.githubusercontent.com/364501/222031460-ffb1ecbd-5175-4a42-8470-25285ba5f821.png)


### Steps to reproduce

Try to access the `global_position` of a `Node3D` that's assigned to an exported var.

See that it works at runtime.

See that it errors in the editor with:

> Invalid get index 'global_position' (on base: 'Nil').

### Minimal reproduction project

[tool_test.zip](https://github.com/godotengine/godot/files/10856640/tool_test.zip)

node->set(prop_name, prop_variant);
								continue;
							}
							const Array &array = prop_variant;
							for (int k = 0; k < array.size(); k++) {
								DeferredNodePathProperties dnp;
								dnp.path = array[k];
								dnp.base = node;
								
								dnp.property = String(prop_name) + "/indices/" + itos(k);
								deferred_node_paths.push_back(dnp);
							}
						} else {
							node->set(PackedScene::META_POINTER_PROPERTY_BASE + String(prop_name), prop_variant);
							if (!Engine::get_singleton()->is_editor_hint()) {
								
								DeferredNodePathProperties dnp;
								dnp.path = prop_variant;
								dnp.base = node;
								dnp.property = prop_name;
								deferred_node_paths.push_back(dnp);
							}
						}
						continue;
					}
					ERR_FAIL_INDEX_V(nprops[j].name, sname_count, nullptr);
					if (snames[nprops[j].name] == CoreStringNames::get_singleton()->_script) {