My laser illiteracy is showing so forgive me if this is a stupid question…
Can you set different focus heights for different pieces in the same cut? I was wanting to upload a project needing thick and thin material. I want it to cut a thick draftboard pieces and then have it cut medium draftboard pieces without having to restart the machine. (I’m just lazy like that and tired of running back and forth lol.) I wasn’t sure if the machine can correctly adjust focus heights in the same cut.
Sure. Shouldn’t be an issue. Your placement will be off more than normal for one of the two materials. Not sure what would happen (accuracy wise) if you set your thin material height, placed it, then set your thick material height and then placed that part of the design. Just make sure they are separate operations and set the focus height up correctly for each operation.
Thanks JB. I figured one or the other placement would be slightly off and I can live with that. (Living with that now anyways lol.) I just wasn’t sure if the quality would suffer becasue the GF wouldn’t focus accurately on the second setting. This will save me a few dozen trips back and forth 
An interesting question. We are told that setting the focus manually overrides the measurement but it still takes a measurement anyway. If it completely ignores it you will be fine if you measure your materials and put that in the manual focus settings.
If you use a 20x12 artboard/canvas, you can do absolute positioning, which might or might not help you for this.
Yes. I did it with the foamcore testing. The machine will pause, adjust the focus, and continue, so don’t be alarmed. (Scared the crap out of me the first time it did it.) 
I put materials of different thickness in frequently to save time, especially if I am using scraps that I will later assemble. Placement can be an issue since lid camera image is based on an entered height. Might be a good chance to test how image placement in regard to a focus height that is off works. If the scrap allows a 3/8" margin of error, that’s generally good enough for placement. Since you can manually enter the head focus for each operation, you are good to go.
One interesting test would be to not worry about entering thickness and see if auto focus changes for the different materials as @Jules mentioned, or the state of the continuous auto focus thing . Still trying to comprehend all these parameters, then you have the red laser range finder going off outside of the material when there are gaps or the scraps are small.