In Auto Layout, layers are ordered based on their position in the auto layout. This coupling seems unnecessary. In normal frames and groups, layer order (which also determines which layers will overlap others) is independent of the layers’ X/Y coordinates and size, but in Auto Layout, there is no option to change the layer order without also changing the layout.
Usually when I encounter this issue, it’s because I’m trying to pop something from the middle of the list out in front of the others, e.g. a tooltip that’s displayed on hover.