Why is Chabura prohibited on Shabbos?

I recently started learning כתובות and therefore from time to time I will post interesting things that come up. Believe it or not, the gemara in כתובות 5-6 is very relevant to this question about Chabura.

There are 3 opinions in the Rishonim why chabura (making a wound where blood comes out) is prohibited.

1. Rashi in Shabbas 107a states that the issur is צובע, the blood will color the skin
2. Tosafos in anumber of places states that it is because of נטילת נשמה they say מה לי קטלא כולה מה לי קטלה פלגא
3. The Rambam writes that it is based on מפרק which is a תולדה דדש

The gemara in כתובות on 5b is difficult for all 3 explanations. The gemara states as follows. The students asked: Is it permitted to have the first relations on Friday night because the blood is considered "Mifkad Pakid - held back", (and therefore NOT a chaburah) or is it forbidden because the blood comes from a "Chaburah - wound" (extracted from the membrane itself)?

In other words the gemara says that in a situation of "Mifkad Pakid - held back", there is no problem of Chabura. As an aside this is one of those problematic gemaras with regards to science, we know medically that "Mifkad Pakid - held back", is simply not true. The blood comes from the tearing of the membrane and it is like any other wound.

Let us analyze how each of the Rishonim will deal with the Gemara's distiction.

1. According to Rashi this is very difficult. If the prohibition of chabura is based on צובע who cares where the blood comes from, bottom line, his action is causing the blood to be released and color the skin. Therefore, even if it is Mifkad Pakid it should be prohibited. The Minchas Chinuch asks this and leaves Rashi וצ"ע.
2. According to Tosafos we can expain the distinction as follows. Why is causing a wound considered like killing? Because the Torah says כי הדם הוא הנפש. Therefore causing a wound that bleeds is like partially killing someone. However, this only applies to דם נפש, blood that is part of the regular circulatory process, however if the blood here is Mifkad Pakid, then it is already separated from the body and therefore is not considered דם נפש and it is permitted.
3. According to the Rambam this is very difficult. The Gemara and the Rambam himself paskens this way, states that even where the liquid is Mifkad Pakid there is an issur of מפרק, this comes up both by milking as well as by squeezing grapes and olives. Therefore, why here if the blood is Mifkad Pakid is it permitted. The acharonim give various difficult answers. The best answer is probably the following.

There are 2 aschools of thought in the Rishonim how to deal with a contradiction between 2 gemaras.
1. The 2 sugyas argue with each other
2. Find some distinction either in din or in the case to answer the contradiction.

The Rambam followed approach 1. Contradictions in gemaras did not really bother him. Therefore this gemara in כתובות is against the Rambam, but the Rambam will say that we don't pasken like that. The Baalei Hatosafos really popularized approach 2 and since then that has been the dominant approach. This has led to many explanations given to difficulties in the Rambam using this kind of approach which is really not the Rambam's approach.

I remember reading an article in Tradition about R' Chaim and the Rambam and the article made the following point. The Rambam wrote a number of teshuvos to the חכמי לוניל, who asked various questions on the Mishne Torah. Instead of giving Lomdishe R' Chaim type answers the Rambam gave baale batish answers (the girsa is wrong, the 2 sugyas argue with each other, etc.). It was said among the Briskers that R' Chaim didn't like these teshuvos. This is not to say that R' Chaim's explanations in the Rambam are wrong, rather to point out that the Rambam most probably had a different approach in learning.