### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### Minimal reproduction project

N/A
List<String> property_names;
						for (const PropertyInfo &E2 : pinfo) {
							if (E2.usage & PROPERTY_USAGE_STORAGE) {
								property_names.push_back(E2.name);
							}
						}
						
						for (const KeyValue<StringName, Variant> &E2 : E.value.property_table) {
							if (property_names.find(E2.key)) {
								modifiable_node->set(E2.key, E2.value);
							}
						}
						
						for (const ConnectionWithNodePath &E2 : E.value.connections_to) {
							Connection conn = E2.connection;
							
							Node *target_node = cast_to<Node>(conn.callable.get_object());
							
							
							
							if (!target_node || !target_node->is_queued_for_deletion()) {
								target_node = modifiable_node->get_node_or_null(E2.node_path);
							}
							if (target_node) {
								
								Callable new_callable = Callable(target_node, conn.callable.get_method());
								if (!modifiable_node->is_connected(conn.signal.get_name(), new_callable)) {
									ERR_FAIL_COND(modifiable_node->connect(conn.signal.get_name(), new_callable, conn.flags) != OK);
								}
							}