From the Second Layer 'Twilight Sanctuary' to the Third Layer 'Crimson Court', one originally needed to reach the 'Courtyard Stairs' located at the center of the sanctuary.
It's a large central elevator capable of carrying nearly a thousand people and a large amount of supplies up and down at the same time. This is also the transport tool that passes through the nearly kilometer-thick 'shielding layer' between the Second and Third Layers. If one were to attempt digging with brute force, the solidified rock layer nearly a kilometer thick would require considerable effort and time even for the Third Energy Level individuals.
After all, the first two layers of the Exotic Species Research Institute are essentially civilian facilities, designed as a sanctuary to survive the apocalypse, whereas the Third Layer and below constitute the true 'Exotic Species Research Institute'.