What is the difference between a sacral dimple and a pilonidal cyst/dimple?

Same. Question of semantics. Some use other names based on depth.
Cute vs. not so much. Pilonidal "dimples" are properly called "pits", are always in the midline in the gluteal cleft, and are where infection of the pilonidal cyst starts, as dislodged hairs can work themselves into these. On the other hand, "sacral dimples" are higher on the lower back, usually on both sides (not in the middle). There is no skin opening, just the dimple. They look kind of cute in a bathing suit.