I look at chakras the same way I look at Quantum Science, Molecular Sciences and Mind Sciences, and perhaps coaching as well. Be it the Theory of Relativity. Heizenberg’s Uncertainty Theory, the existence of Black Holes and Wormholes (Stephen Hawkins & Others), Epigenetics (Bruce Lipton) as different from Behavioral Genetics, or psychiatric theories on Dementia and Depression, all these are theories that are supported by empirical evidence rather than controlled Newtonian scientific proof. Yet, all these are fully accepted. So are several theories in molecular biology and neural sciences that support the mind-body connection.
As for medical evidence, practically every experienced doctor believes that the mind influences the body, though there is no proven evidence. There is a widespread condition of myofascial pain. In this condition, the pain is transmitted through a sheath beneath the skin rather than the nervous system. Despite many doctors not accepting this, physiotherapists cure this condition through multiple other interventions. Unfortunately, the fascia seems to disappear when we stop breathing, so anatomical study of cadavers do not help establish a connection. Many psychiatric theories are not evidenced through scientific rigor, yet are accepted as being true, even when results vary when practiced.
I believe that scientific and medical methodologies also have limitations in establishing cause and effect connections. Chakras are not the only area where this limitation applies. There is a large mass of published empirical evidence, some cited below, to support the existence of energy centers in the body that influence the mind-body system.
Chakras are invisible. Perhaps they are metaphors for energy. Matter and energy are integrally related as accepted by science. Body is matter and is visible. Chakras are energy and are invisible. Whether there are 6, 12 or more chakras, where they are and how they influence our body and mind are debatable. However, several postulated theories are available in Vedic scriptures.
I studied chakra meditation for over 20 years. I suffered through bad practices I learnt from New Age authors from California. I then turned to ancient Hindu Buddhist scriptural wisdom to explore them safely. All I know from personal experience is that we have energy centers in different parts of our body, which when aroused have impact on both body and mind functions. I have used chakra energization extensively in both emotional and physical healing. As with many things with our mind-body system, such as emotions and even illnesses, controlled experiments do not work in producing reproducible results.