I never use set focus on glass/transparent, and there are other materials where the automated system fails - hence I made this some time ago, and use manual.
In the case of irregular objects where I had the tray removed (shot glasses, spice jars), I would use scraps of material to get the object propped to the desired height, which the little tool can help you determine. Remove the object, take a few measurements, repeat in my design app to build the jig. Then I would cut a piece of shipping box to create a repeatable “locator” that fits squarely against the front corner. I actually always used the right, but most people would say the left would be better.
So my jigs for shot glasses and spice jars are two pieces - and each has an accompanying file with the rough outline of the shape which is set to ignore, used simply for aligning the actual image(s) to be engraved.
The precise locating of the outline was determined by putting a piece of masking on the object and hitting it with a small target (I just use the camera calibration X in a O) roughly located using the camera - and in order to make that quick and simple, I usually make my jigs so the surface of the object is relatively close to the center of the machine under the camera.