1) It is important to see Tosfos to Yevamos 56a, DH li'Devarim. He writes that the Chidush here is that Bi'ah b'Shogeg acquires the Yevamah. See the Mishnah in Yevamos 53b, and the first Rashi there, that the Yavam thought that the Yevamah was his wife or another woman. Normally, such a Bi'ah would not effect any Kinyan. The Chidush is that such a Bi'ah does have the power to make Yibum. But since an inadvertent Bi'ah does make Yibum, Tosfos writes that it is logical to say that the Torah included such a Bi'ah only so that it can work only for the minimum amount of things possible -- namely, only for matters which are stated explicitly in the Parshah of Yibum.

2) The Gemara (Yevamos 56a) states that what is explicit in the Parshah is that the brother-in-law inherits the property of his deceased brother. He would not inherit the Yevamah if she died. All that happens is that the Yavam takes the place of his dead brother. This is the idea of Yibum -- that the brother takes the place of the Niftar. In addition, once the brother has done Yibum with her, she will not have to do Yibum with someone else; for example, if the second brother later dies, but he already has children from a different wife, the Yevamah is now exempt from Yibum.

3) The idea is that the biyas zenus is considered as a minimal biyah. Rashi here in Sotah calls it a "biyah kol dehu". Rashi Yevamos 56a DH Kanah and 56a DH Min Hanisuin calls it a "biyah geruah"; it is a bad, weak, biyah and would not normally possess the din of a proper biyah that can effect kidushin. Since it only makes Yibum because of the special Parsha in the Torah of Yibum, it follows that it has a limited capability, and only helps for things stated explicitly in the Parshah.

4) I think that this Sugya about Shmuel, and Rashi here, is a very good source for a statement made by Rav Chaim Soloveitchik zt"l ("Stencil" on Shas). (This is in Maseches Yevamos. In the old edition of the "Stencil" it is on page 7, and is the second item, "b'Inyan Yibum," which is referred to as "item 10" in Maseches Yevamos.)

5) This is actually connected to the first Mishnah in Maseches Kidushin, which states that there are three ways of carrying out standard Kidushin: Kesef, Shtar, and Bi'ah. The Mishnah concludes that there is only one way of carrying out Yibum -- this is Bi'ah. Tosfos (DH ha'Yevamah) cites the Gemara in Kidushin 14a that Bi'ah effects Yibum, but Kesef and Shtar do not effect Yibum.

6) Rav Chaim says a Chidush, that it is not only Kesef and Shtar which do not apply to Yibum, but even the Kinyan of Bi'ah for Yibum is different from the Kinyan of Bi'ah for standard Kidushin. Rav Chaim writes that Bi'ah is a new Kinyan of Yibum. He cites a proof for his Chidush.

7) I want to suggest another source from our Sugya for Rav Chaim's Chidush. The point is that we know already that there are differences between the marriage of standard Kidushin and the marriage of Yibum, as we see from the fact that there are three ways of doing standard Kidushin and only one way of doing Yibum. We now learn from Shmuel's Shitah that even in that one way there are differences. In fact, we see from the Mishnah (53b) that even a Bi'ah of Shogeg or Mezid can make Yibum, while such a Bi'ah could not make a standard Kidushin. Shmuel adds that since it is only a Bi'ah "Kol Dehu" (minimal), it follows that she does not become his wife in every respect. Since this is a special Kinyan for Yibum it follows that she becomes his wife only with respect to things which are directly unique to Yibum.

(I based this idea on the Encyclopedia Talmudit, entry Yibum, volume 21, page 281, note 11, and page 341, note 814.)

Kol Tuv,

Dovid Bloom