The gemaruh deals with the argument if the Flood ever took place in Israel. As there might be dead bodies buried in the deep ground and therefore cause Tuma problems with the dealings of the Parah Adumah.
The problem if there is a dead body from the time of the Flood is unclear to me. Since they were all Non-Jews, and even though it is an argument in the gemaruh, we Poskin that non-jews do not Metameh BeOhel.
And if the bodies we are referring to are deep, deep, in the ground this should be an Ohel problem ??
Are we to differentiate between a dead body and a burial plot for non-jews, or that maybe Paruh Adumah is special regarding these Halachot ?? ( I have never heard of such differences ).
You are in good company! Keren Orah, Yefe Enayim, Mitzpeh Eisan and Hagahos Ya'avetz all ask this question and leave it unresolved.
(a) It is true that Rebbi Shimon (Yevamos 61a) says that non-Jewish corpses are not Metamei b'Ohel. However, that alone does not present a problem, since our Gemara may accept the opinion of the Rabanan (ibid.) as Halachah, and they maintain that a non-Jew is Metamei b'Ohel. (Many Rishonim rule like the Rabanan.) This indeed seems to be the intention of Tosfos and the Shitah Mekubetzes Nazir 54b DH Eretz ha'Amim, with regard to those who died in the Mabul.
However, the problem that bothers the Acharonim is that Tosfos in Yevamos (61b DH Kivrei) proves from the Gemara in Nazir 54a that even the Rabanan agree that a Mes from before the Torah was given is not Metamei b'Ohel (but only b'Maga). If so, what Tum'ah exists from those who died in the Mabul? Tosfos in fact asks similar questions from a Gemara in Bava Basra 58a, and Nidah 70b, but he does not raise the question from our Gemara. We therefore have two questions to answer: Why are we concerned about Tum'ah coming from the Mesei Mabul, and why didn't Tosfos (or any of the Rishonim) ask this question?
(b) Most probably, the reason the Rishonim do not ask the question is because the Gemara might be talking about Tum'as Maga. That is, the concern was that the pieces of bone became mingled with the soil such that they would touch the Parah either before burning or as it is being burned.
However, this does not answer our other question, since it is clear that there are at least some Rishonim who had no trouble with the understanding that the Mesei Mabul would be Metamei the Parah through Ohel (for example, the Tosfos in Nazir 54b cited above, and Rashi in our Sugya who mentions Kever ha'Tehom).
(c) On the other hand, to answer the question of why the Mesei Mabul had Tum'as Ohel, your suggestion that it is a Ma'alah of Parah Adumah is unlikely. Ma'alos normally involve being concerned for something that is highly unlikely to occur. However, if something is not Metamei in the first place, why should the Rabanan give it Tum'ah as a "Ma'alah"?
We may suggests two other answers to your question.
1. Tosfos in Nidah 70b DH v'Ein supplies an answer to our question (see also Tosfos Nazir 54a end of DH O). Tosfos there suggests a novel explanation for the Gemara in Nazir, according to which even Rebbi Shimon agrees that both Jews and non-Jews were Metamei if they lived before Matan Torah, since there was no difference between the two yet at that point. He writes that when the Gemara in Nazir says that a "Kever Lifnei ha'Dibur" should not be Metamei b'Ohel, it is referring to a Jew who died after Matan Torah but before the Parsha of Parah Adumah was given (see Maharsha there).
2. The Vilna Gaon (Aderes Eliyahu, Parashas Chukas) writes that although a Nochri is not Metamei b'Ohel, one is Tamei if he touches the top of the grave (or the dirt above the burial plot) of a Nochri (even without touching the corpse itself). The reason for this is because touching Tum'ah Retzutzah is like touching the Mes itself! (See Ohr Same'ach Hilchos Tum'as Mes, who discusses this Chidush at length.)
(Tum'ah Retzutzah refers to a Mes that occupies a space that is less than a Tefach in length, width and height, which is not considered an Ohel. Tum'as Mes in such an area is called "Tum'ah Retzutzah" (smashed or squashed Tum'ah). Such Tum'ah is "Boka'as v'Olah, Boka'as v'Yoredes," i.e. it "breaks through" (Boka'as) the enclosure and goes straight up and straight down, as it were, all the way to the heavens and down to the center of the earth. (This answers your question about graves deep underground, by the way; yes, they are certainly Metamei what walks above them.) If a grave has less than a Tefach of space between the body and the ceiling of the grave, the Tum'ah inside it is Tum'ah Retzutzah. The Tum'ah is Metamei everything that is above it and below it until something is Chotzetz, thus keeping it inside an Ohel.)
According to the Gaon, it is clear that those who died before Matan Torah will be Metamei those who touch the dirt above their graves (e.g. the Parah Adumah), since even these Mesim are Metamei b'Maga.