al derech hateva. And that is that the import of אֵם יַעֲקֹב וְעֵשָׂו was that they shared a single placenta in Rivka's womb. For al derech hateva, even twins each have their own placenta, but do not share one. But the wonder here was that they shared a single placenta. And this can help explain vayitrotzetzu habanim bekirba, how they struggled in the womb, and also why it was more than other people's pregnancies.
It appears that this is all dependent upon a medieval understanding of medicine. In fact, sometimes twins have separate placentas and sometimes they share a single placenta. This is due to the fact that the placenta itself develops from the fertilized egg. Therefore, fraternal twins never share a placenta. But identical twins sometimes share a placenta. It depends when the twins split off. If it splits very early, then each might develop its own placenta. But that occurs only 1% of the time. In 99% of cases (apparently), they share a placenta. But even within this shared placenta, there can be two separate sacs (amnions) within the placenta. This occurs 60% to 70% of the time, when the split occurs about 2 days in, and such twins are called monochorionic diamniotic twins.
When Rabbenu Bachya said that al derech hateva even in the case of twins they have different shilyas, it is possible that he was conflating fraternal and identical twins, such that in his (or medieval science's) understanding, this was indeed the case. And not always is it possible to tell the difference between fraternal and identical twins, especially when there is no DNA test. And it is possible that by shilya he meant the amnion rather than the placenta. Indeed, if they have separate sacs in the placenta, they could not very well struggle, now could they? And so we have a large percentage of twins which are actually fraternal. Of the identical, 99% would have one placenta -- assuming of course that medieval environmental conditions would not shift this somehow -- and of those, only 30%-40% would share a single amnion. So it is understandable that he would label this derech hateva, while sharing a single placenta and amnion would be a peleh.
But it is still entirely without the realm of natural possibility. However, what Rabbenu Bachya likely does not realize is that to say they shared one shilya, and one amnion, one would need to say that Yaakov and Esav were identical twins. Perhaps one can say this. The divergence later, stressed in midrash, can then be even further developed. The fact that Esav was born hairy and ruddy while Yaakov was not could be attributed to environmental factors.
Ibn Ezra has a related suggestion. He also subscribes to the medieval scientific belief that each twin must have its own shilya. But he says that it was wondrous that the placentas (or else sacs) opened up at the same time. What is driving Ibn Ezra is presumably the fact that Yaakov grabbed onto Esav's heel, which would not be possible if both shilyas were closed. Indeed, we might seize this reason as well to reinforce Rabbenu Bachya's suggestion that they shared a single shilya. And then determine that they were identical twins. But according to Ibn Ezra, they could well be fraternal twins.
There is one extra twist. There is a Rashi which makes it clear that Yaakov and Esav could not be identical twins. On Bereishit 25:26, Rashi reads:
And afterwards, his brother emerged, etc. I heard a Midrash Aggadah that interprets it (the verse) according to its simple meaning: He (Jacob) held onto him lawfully, to restrain him. Jacob was formed from the first drop and Esau from the second. Go forth and learn from a tube that has a narrow opening. Insert two stones into it, one after the other. The one that entered first will emerge last, and the one that entered last will emerge first. The result is that Esau, who was formed last, emerged first, and Jacob, who was formed first emerged last, and Jacob came to restrain him so that he (Jacob) should be the first to be born as he was the first to be formed, and he would open her womb and take the birthright by law. — [From Gen. Rabbah 63:8]I do not believe that medically speaking, the order of conception determines birth order of twins. Or that it is so narrow that it is a single tube.
But I found this Midrash Rabba in 63:11. Rashi develops it somewhat, and in the midrash it is actually the matter of a discussion between a presumably Roman matron and Rabbi Yossi ben Chalafta. There are several such discussions between them. (See here.) So underlying this might be a discussion of who is prime, the Romans or the Jews, (conceptual) descendants of Esav or the descendants of Yaakov. If so, it is unclear whether this was truly intended literally. It is certainly possible that it was. We need to know more about the contemporary science to make such a determination.
And Rashi changes the midrash slightly in citing it, making Yaakov attempting to obtain what is rightfully his. And this then is true to a running theme in the Biblical text as well as other midrashim, in which Yaakov appears to be doing something slightly askew (stealing the blessing, coercing Esav to sell the birthright, getting the best of the deal from Lavan), but in each case the argument can be made that he is the rightful person to receive each of these things. This midrash just reads this even into the grabbing at the heel at birth, emphasizing this message even to the significant moment of birth. In which case, as noted, this midrash need not be intended as absolutely literal.
But at any rate, if Yaakov and Esav came from different drops of semen, then they would have to be fraternal twins. In which case they could not, at least al derech hateva, share a placenta or an amnion.
This is an interesting Rashi, though. It does not appear in the first printing of Rashi. And an early manuscript, rather than having "I heard a Midrash Aggadah," has "I, the scribe, heard a Midrash Aggadah." In which case Rashi never said this, but this was a comment inserted by a scribe, which eventually worked its way into the main text of Rashi. If so, we do not know that Rashi himself would be forced to argue with Rabbenu Bachya and claim that they were fraternal twins.