### 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
switch (tool_menu->get_item_id(p_idx)) {
		case TOOLS_ORPHAN_RESOURCES: {
			orphan_resources->show();
		} break;
		case TOOLS_CUSTOM: {
			if (tool_menu->get_item_submenu(p_idx) == "") {
				Callable callback = tool_menu->get_item_metadata(p_idx);
				Callable::CallError ce;
				Variant result;
				callback.callp(nullptr, 0, result, ce);
				if (ce.error != Callable::CallError::CALL_OK) {
					String err = Variant::get_callable_error_text(callback, nullptr, 0, ce);
					ERR_PRINT("Error calling function from tool menu: " + err);
				}
			} 
		} break;
	}
}
void EditorNode::_export_as_menu_option(int p_idx) {