In the saṃyukta on the Four Bases of Mindfulness, contemplating the body as the body is never connected with the breath. The only sūtras that make this claim are those that are associated with ānāpāna. In the SA / SN, the saṃyukta for the Four Bases of Mindfulness describes the Four Bases of Mindfulness only as abstract contemplations, and never as ānāpāna, impurity contemplations, etc.
In my opinion, those are later additions that were basically “bolted on” to the Four Bases of Mindfulness, probably because the Four Bases of Mindfulness were considered the orthodox form of mindfulness that everyone agreed was definitely Buddhism. Mindfulness in the SA / SN is generally said to be summed up as the Four Bases of Mindfulness, and mindfulness is also repeated a number of times in the 37 dharmas conducive to Bodhi.
Also, the āgamas do not generally translate the phrase as “body in the body,” or anything like it. They translate it more like “body as the body,” or “body, body.” In this stock phrase, I don’t see any implication that there is a body inside another body, like a subtle body.
That is not to say that esoteric anatomy is irrelevant to early Buddhism, but just that it doesn’t take this form. As far as I can tell, the subtle body in early Buddhism is best represented in terms of the skandhas and the elements.