The skull shows when the opponent is out of time (and he is not on vacation). When the skull shows, it is clickable, perfectly within the rules, and the opponent has lost his game.
Keeping the thinking time is a part of chess, and agreed upon when the game starts. Failing to do so gives the other player the right to skull the player out and collect the win.
This has nothing to do with who is about to win if the game continues.