The layers are still useful for the reason stated: to make more than one version of a map, in this case to make player handouts. For instance, you can have all your labels on one sheet, with a single set of effects applied to them, but the GM info is on one layer while the player info is on another, and the information shared between both is on a third. You could do it with three sheets, but that requires thrice the system resources to draw, not to mention having to set up the effects three times.