It’s important to understand the metaphorical nature of the language used in yoga philosophy and anatomy. It can be easy to let concepts like chakras, prana, etc. obscure the greater truths that they’re used to illustrate, but remember that wisdom from a different time, language, and culture is still wisdom.
The purpose of yoga anatomy isn’t to articulate a 100% scientifically descriptive discourse by appropriating Indian mysticism. Rather, its purpose is to articulate a holistic perspective of the body/mind and its inner workings that can be understood from within the greater context of Yoga.
Acknowledging this distinction allows the truth of both science and yoga to do their jobs without one negating the validity of the other.
Just as understanding the Scientific workings of the body need not diminish one’s awe of Nature, the pre-modern imagery of the Yogic explanation need not be misinterpreted as supernatural justification for natural phenomena.
I’ve found that when it’s not immediately clear to me how a yogic explanation of the body can be scientifically translated, the answer is to practice more asana. Eventually, the truth becomes clear. Indeed, such clarity is part of the power of yoga asana.