Something doesn't make sense to me. What is a channel exactly? Air goes into the lungs, the oxygen is taken into blood stream. The yogic method of channels and winds uses channels that are not lungs or blood vessels. How the three channels meet at the base of the body is not connected to a cavity or passage where gas could travel.
A channel is a channel: veins, arteries and nerves. You can add to this the lymphatic system, though they are considered to act as a support for bring moisture to the nervous system among their other functions.
A cakra in this view is any place in the body where there are clusters of arteries, veins and nerves. You can readily see five such clusters in the body. There are many more.
The channels we visualize are just a method -- why? because when we are visualizing ourselves as a deity, we visualize our bodies as completely hollow, made of light, with no internal organs.
The explicitly stated point of view of Tibetan Medicine is that the avadhūtī is all channels of air i.e. arteries; the rasanā is all channels of fire i.e. the blood vessels, and the lalanā all channels of water i.e. the nerves in the body. This is detailed at length by Zurkhar Lodo Gyalpo, is based primarily on the understanding of the anatomy of the body indicated by the Third Karmapa in his Zabmo Nangdon and reinforced by Desrid Sangye Gyatso. The latter two were both great Dzogchen masters as well though, Zurkharwa was not.
For example, the Kagyu Historian, Thubten Phunstog, has written an interesting commentaries on Tibetan Medicine, Six Yogas of Naropa, and well as Zabmo Nangdon. He makes the case that if channels are not physical structures in the body, then practices like gtum mo would have no effect. Then there is the very interesting doctor in Golok, Menpa Tenzin, who wrote a book based on doing many years of dissection of cadavers which contain very detailed drawings of his research. One may think this unnecessary given Netter's Anatomy and so on, but it is interesting -- and his dissections were guided from a Tibetan Medical perspective. He really explained this principle to us very well when we are interning in Xining. He is a disciple of Khenpo Munsel and In Tibet, he is a well respected Dzogchen master.
In reality, the three channels meet in each of these five (or six) locations in the body, according to the presentation I gave above from Kalackara. This simply means you will find clusters of arteries, veins and nerves at these locations in the body. Again, to restate, when we are doing deity yoga, our bodies are conceived to be hollow -- thus we visualize the channels in various ways depending on what system we are practicing. Hence, according Menpa Tenzin, et al, our visualization does not correspond with the manner in which the three channels actually exist in the body, and more importantly, it does not need to.
The reasons behind this again become very clear when one studies embryology according to Tibetan Medicine, Kalacakra, or Dzogchen Nyinthig. A very good book on this subject has been published by Francis Garret.
However, again, in the West, our idea of ṇāḍis has been very influenced by the acupuncture idea of "meridians" as well as Hindu ideas of cakras and ṇāḍis. The Upanishadic idea of cakras and ṇāḍis is related to the concept of pañcakośa originating in the Taittiriya Upanisha (which makes this idea a bit older than the Buddha's teaching), where they are explicitly connected with the prāṇamayakośa. On the other hand, the Upanishads are very important to understand, because they contain many ideas and concepts which reappear in altered form (i.e. revised in accordance with Buddha ideas) in Vajrayāna, Ayurveda/Tibetan Medicine, and even in Dzogchen.