Set Matte is a very powerfull effect: it allows to use the Alpha (or other channel) of a second layer somewhere in the Comp for a matte.
No need for the matte layer to be above the matted layer!
Set Matte is not looking at the layer at full Comp size, but to the bounding box of the layer content. Which makes it less valuable in many cases.
Add a switch called 'Use full Comp size as layer size', which does just what it says, without the need for precomping.