Good question and I doubt whether this is a complete answer. I will stick to my personal experience. Chakras are very subtle, belong to the astral body. When activated chakras act like mini-brains to take over sensing from outward-bound physical sense organs. They also control the secretions of various glands to regulate body functions that manifest on the physical level. Unless one is born with rich spiritual legacy, chakras start extinguishing as we grow. As a toddler, we struggle physically to learn physical skills to survive. As a teenager, our ego gets built beginning the hardships for the astral body. As adults, we start living by emotions and bring a wholesale hurt and bruise to the astral body. Unaware of it, we rampantly abuse astral body while seeking physical well-being.
Consequently, chakras do malfunction and eventually become redundant. The root cause of many diseases can be found in glandular imbalance the cause of which goes back to weak chakras. (today’s medical research perhaps knows about this or is shy of admitting a subtle element into their “hard” evidence. Knowing this is also inconvenient to the mighty pharmas since there is money in cure, none in prevention.)
But, you have brought out an excellent point. Yes, a displaced, weak or malfunctioning chakra is undoubtedly a result of a person’s wrong physical behavior, wasteful intellectual acrobatics, indulgent emotional swings and utter lack of any spiritual awareness. The health of chakras, and this is important, is definitely an early warning of impending diseases. The whole Ayurveda is based on this premise.
That is why, Yoga Sutra puts as Yoga’s goal “healing of the psyche”.
(Note: chakras are subtle and will not present a medical picture as precise/ vivid as today’s mainstream practice. But, we need to move towards it. Secondly, a high-end philosophising of stalwarts like AmirMourad, also hurts the cause. All the disparate narrations about chakras are due to the developmental phase. Until, one reaches ability to perceive chakras, one has to use some approximation, some guesswork and some experimentation.)