When you remove the honeycomb tray for engraving thick items, you need to elevate the surface to be engraved so that it is within the 1/2" focus range of the Glowforge. Items that have a lip or rim around them are difficult to engrave because the printhead must not hit the rim, but the bottom area to engrave must still be within 1/2" of the lens. I cannot tell from your photos how deep your dish is, but all of your problems are related to proper focus.
There are many posts here in the forum explaining how to engrave without the honeycomb tray.
Here is one recent thread: Keeps changing my thickness and I get and error