i usually think these issues in terms of psychoanalysis because it was the only attempt to make a science of subjective phenomena.
all sciences dismiss subjectivity as something not important/relevant/serious. and try to objectify people through some sort of uniformed/universal discourse that applies for everyone and everything.
in psychoanalysis chakras can be comprehended as an artificial creation made by something called Real castration.
Real castration means that the psyche needs to recognize something as radically exterior first to constitute itself (therefore, something “else/other” becomes “Real” in subjectivity).
this radical exteriority is localized by Freud & Lacan at first through parts of the body that are holes/gaps and that become energetically charged by pleasure. this high voltage of pleasure is localized as exterior (or something that’s “other”) and through iteration/repetition creates a structure in the energy body.
mouth. anus. genitals. gaze. throat. later on, any part of the body (vertebrae/stomach/lungs/etc).
in this sense, chakras are artificial creations and not something inherent or natural.
before any sense of exteriority, there would be a “unified field” that later on gets fragmented into “parts”, these “parts” would be the chakra system.