### 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
if (p_editor->has_main_screen()) {
		Button *tb = memnew(Button);
		tb->set_flat(true);
		tb->set_toggle_mode(true);
		tb->connect("pressed", callable_mp(singleton, &EditorNode::editor_select).bind(singleton->main_editor_buttons.size()));
		tb->set_name(p_editor->get_name());
		tb->set_text(p_editor->get_name());
		Ref<Texture2D> icon = p_editor->get_icon();
		if (icon.is_valid()) {
			tb->set_icon(icon);
			
			icon->connect("changed", callable_mp((Control *)tb, &Control::update_minimum_size));
		} else if (singleton->gui_base->has_theme_icon(p_editor->get_name(), SNAME("EditorIcons"))) {
			tb->set_icon(singleton->gui_base->get_theme_icon(p_editor->get_name(), SNAME("EditorIcons")));
		}
		tb->add_theme_font_override("font", singleton->gui_base->get_theme_font(SNAME("main_button_font"), SNAME("EditorFonts")));
		tb->add_theme_font_size_override("font_size", singleton->gui_base->get_theme_font_size(SNAME("main_button_font_size"), SNAME("EditorFonts")));
		singleton->main_editor_buttons.push_back(tb);
		singleton->main_editor_button_hb->add_child(tb);
		singleton->editor_table.push_back(p_editor);
		singleton->distraction_free->move_to_front();
	}
	singleton->editor_data.add_editor_plugin(p_editor);
	singleton->add_child(p_editor);
	if (p_config_changed) {
		p_editor->enable_plugin();
	}
}
void EditorNode::remove_editor_plugin(EditorPlugin *p_editor, bool p_config_changed) {