### 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
int idx = tool_menu->get_item_count();
	tool_menu->add_item(p_name, TOOLS_CUSTOM);
	tool_menu->set_item_metadata(idx, p_callback);
}
void EditorNode::add_tool_submenu_item(const String &p_name, PopupMenu *p_submenu) {
	ERR_FAIL_NULL(p_submenu);
	ERR_FAIL_COND(p_submenu->get_parent() != nullptr);
	tool_menu->add_child(p_submenu);
	tool_menu->add_submenu_item(p_name, p_submenu->get_name(), TOOLS_CUSTOM);
}
void EditorNode::remove_tool_menu_item(const String &p_name) {
	for (int i = 0; i < tool_menu->get_item_count(); i++) {
		if (tool_menu->get_item_id(i) != TOOLS_CUSTOM) {
			continue;
		}
		if (tool_menu->get_item_text(i) == p_name) {
			if (tool_menu->get_item_submenu(i) != "") {
				Node *n = tool_menu->get_node(tool_menu->get_item_submenu(i));
				tool_menu->remove_child(n);
				memdelete(n);
			}
			tool_menu->remove_item(i);
			tool_menu->reset_size();
			return;
		}
	}
}
PopupMenu *EditorNode::get_export_as_menu() {