As long as the overall height is still below .5” above the honeycomb and
As long as you aren’t trying to use the laser that far over,
you should be just fine.
(All other material specific concerns of course, apply.)
A good many of us use the Set Focus all day every day so we can get the best placement. I would stick a little ruler in there and enter the height manually just to make sure the GF has the proper height from the crumb tray honeycombed area. You could either set it in the “unknown material” area or you could set it in the manual focus height box under the individual step settings.
Watch out for material that sticks out on the sides interfering with the gantry. You can get away with a little bit of overhang, but if you go too far then the mechanism is going to bump into it.
When you cut out pieces that are on the inside, like the center of the letter O, it will fall just a bit.
If you cut the outside of the O before the center, the focus height will be just a little different.
So cut the centers and do engraves and scores before cutting the outlines.