The Mishna speak about a case where the head is separated from the body, R' Eliezer argues with R' Akiva if the head follows the body or body follows the head. The Mishna then speaks about which part of the body we measure from, R' Eliezer says the stomach and R' Akiva says the head. The Rambam in his commentary on mishna explains that R' Eliezer focuses on food since that is necessary to keep the person alive, and R' Akiva focuses on breathing since that is a more desperate need (one can go without food longer than he can go without air).
The gemara makes a point of saying that the first machlokes where the head is separated from the body is not a machlokes regarding the measuring for egla arufa because that is coming up, rather it is a machlokes about Yehoshua's institution that a meis mitzvah is koneh m'komo. It is not clear from the gemara what the opinions would be in a case where the head is separated from the body. But the Meiri points out that the machlokes between the tibur (stomach) and chotem (nose) applies also when the head is separated from the body, whether we measure from the nose or the stomach. The gemara understood that since the language of their dispute is whether the head follows the body or the body follows the head, it implies that they must be arguing about acquiring the 4 amos because regarding measuring we already know that one opinion focuses on the head and the other on the body, so we don't have to make the head follow the body or visa versa.
We pasken like R' Akiva that we measure from the nose, and if the head is separated from the body we measure from the head. This is not because the body follows the head, rather all that we care about in regard to measuring is the head.