You state that the plate is not flat. How tall is the rim?
The Glowforge has a 1/2" focus range. The surface to be engraved must be between .001" and .5" from the lens. With the tray in place, this means anything from a piece of paper to something 1/2" thick can be engraved. Without the honeycomb tray, the surface to be engraved must be between 1.5" and 2" from the floor of the Glowforge. Using the no math focus tool is very helpful. No-Math Focus Ruler
If the lip of your plate is more than 1/2" above the surface you are trying to engrave, you are out of luck. If the printhead clears the lip it will be more than 1/2" from the plate bottom and you will not be able to focus.