If you think of things in terms of thickness and how long the heat will take to penetrate through what you're cooking you'll begin to understand why the recommendation is to pack items in a flat layer. Two steaks side by side are the same thickness as one steak. Cooking two steaks this way will take the same time as one. Two steaks stacked atop each other are twice as thick as one steak, therefore cooking steaks which are stacked will take twice as long (or more.)
You need to make sure the water can move around your cooking vessel, so don't overcrowd your pot.