Yes that's right, it was the same arrangement at all levels. Charlton finished in the relegation zone of the top flight in 1987 but saved themselves by beating Leeds United, I think they were the only club at any level who did that though.
Had Notts got the win they needed at York on the last day of 1986/87, we'd have been in the 3rd tier Play Offs and would have played 2nd tier Sunderland in the Semi-finals, who Gillingham ultimately beat to send them down.