Cement is harder than the stone next to it. On a wall that has stood for two hundred years, that is a problem. The stone gives way before the joint does, and the moisture has nowhere to leave.
Lime is softer than the stone. It breathes. It carries water out instead of trapping it inside. It takes longer to apply and longer to cure. We use it anyway.
It is the difference between a wall that looks fine for five years and a wall that is still standing in fifty.