Describing breathing in terms of “long” and “short” is an issue because it is unclear what is being measured. In modern medicine, these terms are avoided, and pointed out as inadequate for describing the breathing process. Some of the factors that would be used in a modern setting today would be “respiration rate” and “tidal volume”. To improve upon “long” and “short”, I would instead just use “coarse” and “subtle”. Those terms are not accurate enough for modern medicine, but are still better than “long” and “short”.
The description of breathing as “long” and “short” also caused confusion for Indian Buddhists. The most common interpretation of “long” seems to have been that it indicates “coarse” breathing. The most common interpretation of “short” was that it indicates “subtle” breathing.
However, the Vaibhasika Sarvastivadins who held the Mahavibhasa and the seven canonical books of Sarvastivada Abhidharma as authoritative, differed from all other groups in that they interpreted “short” as “coarse”, and “long” as “subtle”. As a result, they changed the order of these two items in the first tetrad of mindfulness of breathing. They were very unique in this regard.
From an older post, this is a relevant passage from the Mahavibhasa (T 1545):
問入出息為先短後長為先長後短耶。答先短後長。云何知然。如施設論說。菩薩初入定時其息速疾。久入定已息便安住。如人擔重經嶮難處其息速疾。後至平道息便安住。故入出息先短後長。 (T 1545, 27: 136a22–27)
Question: For inhalation and exhalation, is ‘short’ before ‘long,’ or is the ‘long’ before ‘short’?
Answer: Earlier it is ‘short,’ and later it is ‘long.’ How do we know this? As the Prajñāptiśāstra says, when the bodhisattva first entered samādhi, his respiration was quick, but after a long time of entering samādhi, his respiration naturally and peacefully abided. This is like a man carrying a heavy load who encounters many difficulties along the way and breathes quickly. If he arrives at an even path, his breathing will naturally and peacefully abide. In this way, inhalation and exhalation are short before and long after.
From this interpretation, we might think that the Vaibhasikas were negligent in their treatment of meditation. But actually the Vaibhasika Sarvastivadins had very detailed and in-depth treatments of the matter. The issue here was simply that they interpreted “short” and “long” in terms of the time of each breath (respiration rate), rather than as a measure of tidal volume.
Other Sarvastivadins who were not part of the Vaibhasika tradition, like the Darstantika Sarvastivada yogacaryas, rejected this interpretation of “long” and “short” and wrote refutations of the Vaibhasika sequence. We can see this in Dharmatrata Dhyana Sutra (T 618), AKA the Yogacarabhumi of Buddhasena of Kashmir. Their presumption was that “long” and “short” refer to “the force of the breath”. Instead of resorting to canonical abhidharma, they justified their interpretation based on “what is experienced”. In their view, the transition is from “long” to “short”, as dependencies are abandoned in meditation.
The two traditions were actually describing the exact same transition from coarse breathing to subtle breathing. Both were also describing the transition from subtle breathing, to breathing at the pores, and finally abandoning breathing. They were just using different terminology for the first two stages, based on totally different presumptions about what “long” and “short” refer to.