That’s the fanciest jig setup I’ve seen! Great job! 
This is the problem spot with the idea. It’s great until the tray shifts or you put it back in a slightly different place.
We’ve discovered that if you include any vector cut work and raster engraves together into a single SVG or PDF file, the operations maintain perfect alignment relative to each other.
So for complete accuracy, you can create a rectangle the dimensions of the iphone, align your engraving inside of that using the alignment tools in your drawing software, and then save the file. When you bring the file into the Glowforge interface, you cut the rectangle out of some scrap material that you have fixed into position for the span of that operation, then drop the phone into the cutout, set the cut to ignore, and set the engrave to process. It gives perfect alignment for the duration of the job, as long as you don’t move anything on the screen, or move the backing material while the job is being processed. (And it works out at the edges too, no matter how far off the after-image appears to be.) 
If you’re doing multiples of the same object, you can just cut one hole and drop another phone into the hole for engraving as soon as the first one is done - the relative positions are maintained until you close the file in the app.
There’s a tutorial with a little more description here, it’s just a lot easier to get that perfect alignment in the drawing software that was created for the express purpose of doing that kind of thing: