Unified Transform is great but the preview does not follow the layer list order, instead the preview is always drawn completely over the top of the other layers regardless of the layer list order.

I use Gomp to make mosaics of aerial photos. I can have a situation where I have two layers with a small gap between them that I need to put a part of another layer into. All I need to be happening in the transform is the preview shows me the part of the third layer, the one that is being transformed, that is "underneath" the other two layers because that is how it will be displayed because the other two layers are above it in the layer order.

Unfortunately with the preview being drawn over the top of the other layers, because this preview covers over the other layers, it is very hard to see the edges of those layers to line up the transforming layer with them. So this makes the task very difficult to accomplish.

I have a recollection that you run into the same problem with layers that are masked off in part. The effect of the masking actually disappears during the transform, also making it quite difficult to accomplish.

It's so easy to drag the layers into the correct order before editing them so I do not see this as being difficult to implement.