Understood perfectly. 
The GFUI does not order operations according to Layers. It uses a combination of operation, color and the where the layer falls in the stack. (A bit complicated.)
The rules run:
Engraves will show up at the top of the thumbnail column.
Cuts show up below. (Cuts have to be converted into Scores manually at this point in time, so no way to do it except by hand.)
The use of color will next determine what comes higher or lower in the stack if you have multiple engraves or cut operations set up.
There is a good discussion of how to order operations by color here:
Reasons why you might want to perform separate cut operations is to cut the inside parts out first in a shape if you are afraid it might shift in the air assist. (Good practice to set the interior cuts up to cut first. Just make them all one color, and the outside cuts another color. Black will cut first, Red will cut last.)
Where the actual travel path will follow the Layer stack in Illustrator is when you have a bunch of disconnected paths (layers) that are all the same stroke color - the head generally will go from the bottom of the stack of Sub-Layers to the top. (I think…don’t quote me on that, I haven’t watched it in a while.)
That’s it.