The water supply lines can come from almost anywhere. Sometimes they even come from the side.
Originally plumber installed supply lines a few inches higher than drain. (and few inches wider) But then realized that the drain was too low to fit inside vanity. They raised the height of just the drain rough-in and the supply rough-in are same height they were. So the question is... is it ok that the drain and the supply lines are the same height (from floor)? And if so is this going to pose a problem of them getting the drain rough-in to the bottom of the sink which horizontally will not be directly above the drain rough-in? (See rough sketch attached)