### 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
Ref<ConfigFile> cf;
	cf.instantiate();
	if (!DirAccess::exists(addon_path.get_base_dir())) {
		_remove_plugin_from_enabled(addon_path);
		WARN_PRINT("Addon '" + addon_path + "' failed to load. No directory found. Removing from enabled plugins.");
		return;
	}
	Error err = cf->load(addon_path);
	if (err != OK) {
		show_warning(vformat(TTR("Unable to enable addon plugin at: '%s' parsing of config failed."), addon_path));
		return;
	}
	if (!cf->has_section_key("plugin", "script")) {
		show_warning(vformat(TTR("Unable to find script field for addon plugin at: '%s'."), addon_path));
		return;
	}
	String script_path = cf->get_value("plugin", "script");
	Ref<Script> scr; 
	
	if (script_path.length() > 0) {
		script_path = addon_path.get_base_dir().path_join(script_path);
		scr = ResourceLoader::load(script_path, "Script", ResourceFormatLoader::CACHE_MODE_IGNORE);
		if (scr.is_null()) {
			show_warning(vformat(TTR("Unable to load addon script from path: '%s'."), script_path));
			return;
		}
		
		if (scr->get_instance_base_type() == StringName()) {
			if (_initializing_plugins) {