Treifos and Mystical Approach
12. One may not add to these Treifos at all, since everything that happens to a domesticated animal, undomesticated animal or bird other than these which the sages of the first generations designated and the courts agreed with them, it is possible that it will live, and even if it is known to us from medical practice that it will not live in the end.
13. So too these that they designated and said that they are Treif, even though that we see in medical practice that is available to us that some of them will not die, and it is possible that some of them will live, we have none other than what the sages designated, as it says "according to the Torah that they will teach you."
When we are judging treifos, we must go by the standards set in place by the mesora, not by our observation. Thus, even if we can cure something or prolong its life, now or in the future, that does not change the halacha. Similarly, even if we know through experience that an animal cannot live under the condition, but the mesora is that it is kosher, then we must judge that, in the experience of the first generations, it is possible that the animal will live. Since, they would only need a small number of cases to establish possibility of life, halacha 12 seems reasonable. We have never known a case where one lived, but the sages had heard of it and judged accordingly.
When looking at treifos, if a condition is considered kosher by the first generations, but we now observe it to be treif, then the reality warps around the psak of the first generations and the batei din, and it is physically possible that the animal will live, regardless of the laws of biology. Similarly, if we observe that an animal can live in a certain condition, but the sages said that it was treif, then we must rely on our sages and not change the halacha.
Obviously, the mystical interpretation can be read into halacha 12, but not so well into halacha 13. You cannot apply the principle that reality warps around halacha, because in halacha 13, you are observing the refutation of that. They said that the animal cannot live, but we observe that it can. That is why it does not follow the language from halacha 12 and say "it is impossible that it will live". Yet, halacha 13 begins "so, too", implying that the Rambam saw these two siyifim as extensions of each other. Rather it points out that we must pasken like the sages regardless of the quoted reasons behind the halacha. The quoted reason may only be PART OF THE REASON that the halacha came down as it did.
One might also conclude that, since the Rambam states this as a halacha in Treifos (Sh'chita), it is not a general principle of halacha that we follow the sages when the circumstances change, but it is specific to trefos. When the Rambam learns one halacha out as a general rule, he states so. Yet, the pasuk that he quotes does not have any specific connection to treifos. So why tuck it away here in hilchos shchita? Perhaps it is because shchita is completely defined by mesora, with only a remez in the written Torah. Therefore, the entire matter of shchita is dependent on the ability of the sages to define mesora, even if it will fly in the face of later discovery that they have not anticipated. In other words, whatever they will discover in the future (unknown to the chachamim), the mesora that they transmit in the name of "mesora" will still stand, since they have transmitted only part of the reason for the psak, in order to define and limit the halacha properly. In the introduction to mishna part IV the Rambam lay sout how we can tell what is mesora and what is not.