### 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
#include "editor/plugins/node_3d_editor_plugin.h"
#include "editor/plugins/packed_scene_translation_parser_plugin.h"
#include "editor/plugins/root_motion_editor_plugin.h"
#include "editor/plugins/script_text_editor.h"
#include "editor/plugins/text_editor.h"
#include "editor/plugins/version_control_editor_plugin.h"
#include "editor/plugins/visual_shader_editor_plugin.h"
#include "editor/progress_dialog.h"
#include "editor/project_settings_editor.h"
#include "editor/register_exporters.h"
#include "editor/scene_tree_dock.h"
#include "editor/window_wrapper.h"
#include <stdio.h>
#include <stdlib.h>
EditorNode *EditorNode::singleton = nullptr;
static const String META_TEXT_TO_COPY = "text_to_copy";
static const String EDITOR_NODE_CONFIG_SECTION = "EditorNode";
void EditorNode::disambiguate_filenames(const Vector<String> p_full_paths, Vector<String> &r_filenames) {
	ERR_FAIL_COND_MSG(p_full_paths.size() != r_filenames.size(), vformat("disambiguate_filenames requires two string vectors of same length (%d != %d).", p_full_paths.size(), r_filenames.size()));
	
	
	Vector<RBSet<int>> index_sets;
	HashMap<String, int> scene_name_to_set_index;
	for (int i = 0; i < r_filenames.size(); i++) {
		String scene_name = r_filenames[i];
		if (!scene_name_to_set_index.has(scene_name)) {
			index_sets.append(RBSet<int>());
			scene_name_to_set_index.insert(r_filenames[i], index_sets.size() - 1);
		}
		index_sets.write[scene_name_to_set_index[scene_name]].insert(i);