### 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
ProjectSettings::get_singleton()->setup(ProjectSettings::get_singleton()->get_resource_path(), String(), true);
	settings_changed = true;
}
void EditorNode::_vp_resized() {
}
void EditorNode::_titlebar_resized() {
	DisplayServer::get_singleton()->window_set_window_buttons_offset(Vector2i(title_bar->get_global_position().y + title_bar->get_size().y / 2, title_bar->get_global_position().y + title_bar->get_size().y / 2), DisplayServer::MAIN_WINDOW_ID);
	const Vector3i &margin = DisplayServer::get_singleton()->window_get_safe_title_margins(DisplayServer::MAIN_WINDOW_ID);
	if (left_menu_spacer) {
		int w = (gui_base->is_layout_rtl()) ? margin.y : margin.x;
		left_menu_spacer->set_custom_minimum_size(Size2(w, 0));
	}
	if (right_menu_spacer) {
		int w = (gui_base->is_layout_rtl()) ? margin.x : margin.y;
		right_menu_spacer->set_custom_minimum_size(Size2(w, 0));
	}
	if (title_bar) {
		title_bar->set_custom_minimum_size(Size2(0, margin.z - title_bar->get_global_position().y));
	}
}
void EditorNode::_version_button_pressed() {
	DisplayServer::get_singleton()->clipboard_set(version_btn->get_meta(META_TEXT_TO_COPY));
}
void EditorNode::_update_undo_redo_allowed() {
	EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
	file_menu->set_item_disabled(file_menu->get_item_index(EDIT_UNDO), !undo_redo->has_undo());
	file_menu->set_item_disabled(file_menu->get_item_index(EDIT_REDO), !undo_redo->has_redo());
}
void EditorNode::_node_renamed() {