I added some trays for the individual biomes (all 7) as well as trays to hold the Deck of Secrets and additional tokens.

With these, all items fit neatly in the box with some room to spare (and obviously no lid lift).

You would need to print one of each of these items in addition to the insert by ethern0t; I have not included nor modified any of their work and all of my items are in addition to theirs. Note that the layout is slightly different with the double equipment holder being placed at the back of the large cards and dividers