### 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
p_layout->set_value(p_section, "dock_split_" + itos(i + 1), vsplits[i]->get_split_offset());
		}
	}
	for (int i = 0; i < hsplits.size(); i++) {
		p_layout->set_value(p_section, "dock_hsplit_" + itos(i + 1), hsplits[i]->get_split_offset());
	}
	
	p_layout->set_value(p_section, "dock_filesystem_split", FileSystemDock::get_singleton()->get_split_offset());
	p_layout->set_value(p_section, "dock_filesystem_display_mode", FileSystemDock::get_singleton()->get_display_mode());
	p_layout->set_value(p_section, "dock_filesystem_file_sort", FileSystemDock::get_singleton()->get_file_sort());
	p_layout->set_value(p_section, "dock_filesystem_file_list_display_mode", FileSystemDock::get_singleton()->get_file_list_display_mode());
	PackedStringArray selected_files = FileSystemDock::get_singleton()->get_selected_paths();
	p_layout->set_value(p_section, "dock_filesystem_selected_paths", selected_files);
	Vector<String> uncollapsed_paths = FileSystemDock::get_singleton()->get_uncollapsed_paths();
	p_layout->set_value(p_section, "dock_filesystem_uncollapsed_paths", uncollapsed_paths);
}
void EditorNode::_save_open_scenes_to_config(Ref<ConfigFile> p_layout) {
	PackedStringArray scenes;
	for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
		String path = editor_data.get_scene_path(i);
		if (path.is_empty()) {
			continue;
		}
		scenes.push_back(path);
	}
	p_layout->set_value(EDITOR_NODE_CONFIG_SECTION, "open_scenes", scenes);
	String currently_edited_scene_path = editor_data.get_scene_path(editor_data.get_edited_scene());
	p_layout->set_value(EDITOR_NODE_CONFIG_SECTION, "current_scene", currently_edited_scene_path);
}
void EditorNode::save_editor_layout_delayed() {