Stones have been worn, carried and buried for protection and for healing in most societies this atlas covers, and that much is ancient and genuinely widespread. The system sold today is not.
The modern practice was assembled in the second half of the twentieth century within the New Age movement, and its distinctive components are datable. The pairing of particular stones with particular chakras depends on a colour scheme for the chakras that is itself a twentieth-century Western development rather than an Indian one, as the historical work on the Western chakra system has shown. The vocabulary of frequency, vibration and energy field borrows from physics without using it. The specific correspondence lists differ between authors and have no common source.
The therapeutic claim has been tested in the obvious way. In a double-blind comparison, participants were given either genuine quartz or an indistinguishable glass imitation and asked to report what they felt while meditating with it. Both groups reported tingling, warmth and heightened sensation, and the two did not separate. What predicted the reported effect was the participant's prior expectation, not the material in their hand.
That is a clean result about the specific claim. It says nothing about whether people find the practice calming or meaningful, which many plainly do, and nothing about the older and much better attested use of stones as amulets.
The atlas records the tradition, dates the modern system, and states what the testing found.