### 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 (!bool(EDITOR_GET("interface/scene_tabs/restore_scenes_on_load"))) {
		return false;
	}
	Ref<ConfigFile> config;
	config.instantiate();
	Error err = config->load(EditorPaths::get_singleton()->get_project_settings_dir().path_join("editor_layout.cfg"));
	if (err != OK) {
		return false;
	}
	if (!config->has_section(EDITOR_NODE_CONFIG_SECTION) || !config->has_section_key(EDITOR_NODE_CONFIG_SECTION, "open_scenes")) {
		return false;
	}
	Array scenes = config->get_value(EDITOR_NODE_CONFIG_SECTION, "open_scenes");
	return !scenes.is_empty();
}
bool EditorNode::ensure_main_scene(bool p_from_native) {