From what I've read...
Physical reality is only one small portion of a larger spiritual reality... a good analogy is that we can only see the visible light spectrum, but light itself can take many different frequencies, and they are all happening at the same place and time but we just don't notice them. This is likewise true -- the astral/celestial realms are theoretically "here", but we don't perceive them, it's as if it's another dimension that we can't see, i.e. 5D.
The physical chakras roughly correlate with the actual chakras in the etheric and causal bodies, in 5D you could say. The physical reality is just the appearance of what really goes on in other realms -- the "eyes" and the "brain" actually don't see anything, it is consciousness itself that sees. An easy proof of this is that your sight stays with you when you are OOBE or astral projecting. The physical body and its chakras are just the effects of a greater spiritual reality.
So anyway, things are just the way they are, especially in the physical world. To answer your question, it's the other way around -- it's the physical body that has some sort of connection with the nonphysical bodies and world
Seeking for answers here in the world of effects probably won't do too much good
It's all we have to work with, but we can recognize its limitations and work around them with faith and personal experience.