Man, the Applied Sciences lab sure looks a lot more awesome and advanced with your tileset.
The invisible tree thing seems to be a loading issue. When the second one sprouted it was invisible to people in the vault, but when I teleported there from Torhemn I could see the leaves, and so could others if they'd log out first. Or if I set it on fire.
The adminium drill has been used on the Torhemn Sacrificial pit. While a few more void spots were opened, overall there was limited succes. Under the vault itself no void entrances were discovered. Blame Notch.