### 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
HashMap<StringName, Variant> modified_properties = get_modified_properties_for_node(p_node);
		
		List<Connection> connections_to;
		p_node->get_all_signal_connections(&connections_to);
		List<ConnectionWithNodePath> valid_connections_to;
		for (const Connection &c : connections_to) {
			Node *connection_target_node = Object::cast_to<Node>(c.callable.get_object());
			if (connection_target_node) {
				
				if (!c.callable.is_custom()) {
					ConnectionWithNodePath connection_to;
					connection_to.connection = c;
					connection_to.node_path = p_node->get_path_to(connection_target_node);
					valid_connections_to.push_back(connection_to);
				}
			}
		}
		
		List<Connection> connections_from;
		p_node->get_signals_connected_to_this(&connections_from);
		List<Connection> valid_connections_from;
		for (const Connection &c : connections_from) {
			Node *source_node = Object::cast_to<Node>(c.signal.get_object());
			Node *valid_source_owner = nullptr;
			if (source_node) {
				valid_source_owner = source_node->get_owner();
				while (valid_source_owner) {
					if (valid_source_owner == p_root) {
						break;
					}