The chakras are still a part of “one” system - so it seems inaccurate to say one can replace chakras with “one system”. Chakras is one way to look at energy body, the Dantiens are another. Even the Chakras - they are not exactly same in all schools. They differ in Hatha Yoga, Tantra, Tibetan Buddhism etc. Their utility varies based on whether one follows the fire path, water path and so on.
Essentially, how one’s energy body is structured depends on the method that one is using for cultivation. It is possible at some level to map these various depictions of energy bodies to a certain degree (such as Dantiens, Chakras, five Pranas, Chi-Jing-Shen, Kundalini, Chandali etc.) - but that may be unnecessary for most practical purposes.
In a certain sense, each Chakra mirrors another. And it is said that Sahasrara, the Crown, contains within it all the Chakras. When one is in Nirvikalpa Samadhi - aka Kundalini is refined completely, the consciousness resides in the Crown - one is considered fully Awakened and the lower Chakras are no longer significant. Such a state can be considered as “removal” - and that is the goal of most non-dual Indic spiritual practices.
Some direct-path aspirants - who deal with techniques such as Zen, self-inquiry etc. - completely bypass the energetics and deal only with the mind and consciousness. For such folks, Chakras are “distracting” - but that is just the way they look at it. But even there, the energy body is still there, just that they do not work directly on it.