The stop bar just needs to be low enough to ensure the string has sufficient tension over the bridge that it doesn't slip or move.
Does tailpiece height affect intonation?
It's the height of your bridge that's responsible for your action. Supposedly, lowering the tailpiece will add sustain. Raising it will gain a little tone and give a more "slinky" feel to the strings.
What does raising the tailpiece on a Les Paul do?
“You could raise the bar up and that'll reduce the string angle and make it feel a little bit slinkier. ... Doing that allows you to adjust the tailpiece all the way down to the body, but it reduces the resulting string break angle because of the strings wrapping around and leaving from the top of the stopbar.