Well it probably is a stop cue, but stop by lying down. I guess use whatever works with your dog. Doing down seems more natural for a Border Collie to do.
Just as an aside, on the Martin Clunes program about dogs, when he was with the guy with the sheepdogs, one of his commands for the dog was ‘lie down’ and he used it between each command as in ‘go left’ – ‘lie down’ – ‘walk on’ – ‘lie down’ – ‘go right’ – ‘lie down’ etc. Dog responded beautifully, it was great to watch.
PS I know it’s not go left and right but come by and away to me but can never remember which is which.