Legend has it that Comma Rock was once an island in South Ocean, thousands of years ago. The winds ripped the island apart, and slowly eroded it down over the years to the state that it's in today. Perhaps someday, Comma Rock will no longer exist.
Comma Rock can be challenging to pin down since it is always in motion in the South Ocean, which has a western head-wind slowing you down, and numerous tornadoes. The best way to find Comma Rock is to keep an eye out for what may as well be a spinning top while travelling through the South Ocean. You can also wait until the end of the game, because after a certain point, all sky rifts except for the Dark Rift disappear and the headwind in South Ocean dies down.