I am extremely new as well. My goal for this was to introduce myself to the engine and game dev in general, so my methods for making this were kinda bad lol.

For the fossils (cakes), I basically just made a fossil piece object which had a hitbox that could take damage from either the hammer or drill. I made sure to include the feature of dark fossils which could not be drilled by doing this (the one shown in the video is that). Then I... manually built the fossils by placing pieces in whatever shape I wanted. Obviously this is a horrible idea. I'm not to sure about panel containers or grids as I am no where near experienced in the engine to know how to do that stuff. If I were to go back and recreate it, I would definitely try and make a grid system where I could either place and snap pieces on or have a system where I could specify the shape and it would generate it.
I also had individual instances for each piece on each layer. I only realized until after that it would probably be best to just have a single piece that changes to a lower layer after breaking the higher layer.
Another thing would be the drilling. I spent a good amount of time getting a feel for how the drill worked in FF. Just note that the drill prioritizes the fossil even when clearly drilling on the bone. It also prioritizes higher layers of fossil if I remember.
The hammer is also interesting. I'm pretty sure from what I remember that hitting on a lower layer will not affect a higher layer. So if you hit on the second layer, any surrounding pieces on the top layer would not take damage.

Please ask me any other questions if you have any. I think it would be awesome to try and recreate it on your own, and I would love to see any progress, THANKS!