The upside down tree is just a mental image of how the energy might look to one who could see it in it's active state. From the eye-center downward to the root chakra, it is confined in the central spinal channel--the tree trunk. From the eye-center "upward"--inward--it expands into the astral,
like the branches/foliage of a tree.
The physical body is the "ground" the earth, the outermost plane of the creation, while the sky, where the branches reach to the Sun, are the astral and above. This energy is one of the key ingredients, key vehicles to higher consciousness, one of the reasons for the old "made in the image of God" statement. The "keys to the kingdom of heaven" refer to the methods of meditation used to leave the physical body, and more importantly, leave this consciousness. The eye-center chakra is a big part of that 'key".