Board Thread:Theories and Speculation/@comment-1872728-20160305150743/@comment-734582-20160305175022

Georgio722 wrote: God Tree has roots all over Earth, and when it sucked the blood of everyone, he also sucked the Physical and Spiritual Energy of everyone, which ended in making the first ever chakra. Then it combined the Natural Energy he sucked, and made Sage Chakra. So the God Tree is technically the progenitor of Chakra and Sage Chakra. This is pretty much correct.

What makes Six Paths chakra different from regular is the source.

Six Paths chakra is the power of Death, formed directly from the blood of the fallen. Hagoromo used his powers to free people's spiritual energy. Rather than connecting with each other however, they connected this freed spiritual energy with their own physical energy to form regular chakra.

So:

Six Paths chakra : Soul + Blood of the fallen. Chakra: mind + body.

Similar, but different. Note that one of the Six Paths powers allows for the interaction with the soul, while the Juubi/Shinju has immense vital energy, whereas regular people use their frailer bodies and thoughts/experiences (as explained in the Chunin exams)