I recently read a book about astral projection, where a similar question about the reality of such experiences arose. I quote from the book
"From the mystical point of view, nothing is ‘real’ except ‘Reality’ itself. This world we live in is mere illusion, or Maya, a phantasmagoria of shifting images which have no real existence outside the dreams of the cosmic consciousness. The same thing is true of the superphysical realms, according to this philosophy.
To the man in the street, though—and I include myself in this category—the world is real enough, and the definition of the word ‘real’ must somehow use the world as a basis. Therefore, when we ask whether or not the astral plane is real, we mean ‘real’ in the sense that the world is real. It does not matter whether or not anything is real mystically if we use this yardstick.
Now philosophers will say that the world is real because we experience it, and in that sense anything else that we may experience, including dreams and hallucinations, is also real. That forces us to refine our problem somewhat, and define two types of reality—social and non-social. A dream is real to you since you experience it, but it is not real to anyone else. Hence, it is a non-social reality. It belongs only to a single owner, whereas a speeding automobile, which will become rapidly real to anyone who stands in its way, is a social reality.
The problem, then, is to determine whether astral projection experiences are realities in the social, and not the mystical, sense, and that simplifies everything.”
The above is an excerpt from Steve Richards’ The Travelers Guide to the Astral Plane.
So replace in the above text the concept of astral traveling with chakras, and then we can ask whether chakras are real in the social sense. That is, are they part of a consensus reality of a group of sufficiently trained or skilled people with enhanced vision? If any two people within that group would agree on what they are seeing when looking at the chakras of a third person, then chakras would be part of empirical science. This group could describe what they are seeing as best as they can, so that everything that can be said about chakras could be catalogued and classified, similar to what botanists or astronomers were doing before coming up with any theoretical understanding. Astronomers with their mighty brains and telescopes established that galaxies are ‘socially real’. So it’s not unheard of that the social reality of some things is first established within an expert group of people.
I was musing about socially real siddhis in another thread. Certain socially real siddhis would demand a revolution in our understanding of nature, in particular fundamental physics. The current framework is simply not compatible with e.g. ‘socially real’ chakras, which also explains the generally dismissive stance of the scientific community (as a whole) towards psi research. Extraordinarily convincing data is needed for paradigm changes in fundamental physics, but they happened before and started with anomalies in data. It seems that from a yogic perspective there is little enthusiasm to contribute towards establishing such extraordinary data. And I still don’t understand why there isn’t a moral imperative to do so.
Of course the simplest explanation is that those socially real siddhis that are incompatible with fundamental physics simply don’t exist, which obviates the moral imperative to study them.
I demand from my future self to review this thread should I have anything interesting to say, that is interesting to my current self writing this, just in case my future self might have become uninterested in such topics.