### 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_error) {
		singleton->log->add_message(p_string, EditorLog::MSG_TYPE_ERROR);
	} else if (p_rich) {
		singleton->log->add_message(p_string, EditorLog::MSG_TYPE_STD_RICH);
	} else {
		singleton->log->add_message(p_string, EditorLog::MSG_TYPE_STD);
	}
}
static void _execute_thread(void *p_ud) {
	EditorNode::ExecuteThreadArgs *eta = (EditorNode::ExecuteThreadArgs *)p_ud;
	Error err = OS::get_singleton()->execute(eta->path, eta->args, &eta->output, &eta->exitcode, true, &eta->execute_output_mutex);
	print_verbose("Thread exit status: " + itos(eta->exitcode));
	if (err != OK) {
		eta->exitcode = err;
	}
	eta->done.set();
}
int EditorNode::execute_and_show_output(const String &p_title, const String &p_path, const List<String> &p_arguments, bool p_close_on_ok, bool p_close_on_errors) {
	if (execute_output_dialog) {
		execute_output_dialog->set_title(p_title);
		execute_output_dialog->get_ok_button()->set_disabled(true);
		execute_outputs->clear();
		execute_outputs->set_scroll_follow(true);
		EditorInterface::get_singleton()->popup_dialog_centered_ratio(execute_output_dialog);
	}
	ExecuteThreadArgs eta;
	eta.path = p_path;
	eta.args = p_arguments;