1) My initial response is that Rashi (75a, DH v'Hai) writes that you are forced to say that "Ad Asher Yit'har" is talking about Kodashim because we already have another verse, "u'Va ha'Shemeh v'Taher," which is talking about Terumah.

The one who argues with Rebbi Yishmael learns that it is worse to have two Pesukim which are both talking about Terumah than to avoid making the Derashah on "mi'Zera Aharon" that it teaches that which applies equally to all offspring of Aharon. The latter Limud is only a Derashah, but why should we need two explicit verses that both talk about Terumah?

2) Looking again at this question, I noticed that there are actually two questions here:

(a) What is the reason why the Tana, who argues with Rebbi Yishmael, does not learn that the verse "Ad Asher Yit'har" refers to Terumah?

(b) Why does the Gemara ask on this Tana why we need two Pesukim for Kodashim?

I answered question (a) but I did not answer question (b).

However, I think that, bs'd, according to the answer I gave to (a), the answer to (b) is now obvious.

I explained that the reason why this Tana argues with Rebbi Yishmael is because he did not want to have to say that we have two verses talking about Terumah. But the Gemara now asks, what has this Tana gained? He does not have two Pesukim for Terumah but he does have two Pesukim for Kodashim! So the Gemara asks how is his Shitah any better than Rebbi Yishmael's?

3) Here is a different answer to question (a):

a) I am going, bs'd, to try to prove that the simple meaning of Vayikra 22:4, "He shall not eat from Kodashim until he becomes pure," is that he may not eat from Kodashim, and not that he may not eat from Terumah.

b) I saw this stated most clearly in the Tzelach to Berachos 2b (DH v'Hadar), but first I will cite the relevant Gemara in Berachos 2a-2b. On the last line of Berachos 2a, the Gemara asks, "How do we know that the verse, 'And the sun will come [down] and he will be pure' (Vayikra 22:7), means that the sun comes in and the day becomes pure? Perhaps it means that the light comes [in the morning] and the person becomes pure?"

Rashi (beginning of Berachos 2b) writes that perhaps the verse means that the light of the sun will come up on the eighth day and the man will purify himself by bringing Korbanos and afterwards may eat them.

We learn that on the very first page of Shas, the Gemara is in doubt about whether the Pshat in the verse is like the Tana of Rebbi Yishmael or like the Tana who disagrees with the Tana of Rebbi Yishmael.

c) The Tzelach there (Berachos 2b, DH v'Hadar) writes that the opinion that explains that the verse means that the sun comes down and one may eat Terumah is uprooting the verse from its simple meaning. The verse states, "He may eat from Kodashim," and we explain this to mean he may eat Terumah. The Tzelach writes that to say it is referring to Terumah is to uproot the verse from its Pshat.

d) The Tzelach also cites Rashi in Chumash in Parshas Emor. He does not mention the exact reference or quote Rashi, but I think he may be referring to Rashi on the verse, "And afterwards he may eat from the Kodashim" (Vayikra 22:7). Rashi writes that this is "Nidreshes" in Yevamos as referring to Terumah. This suggests that the Gemara in Yevamos is a Derashah, but the simple Pshat is that it refers to Korbanos.

e) So now we may say that the Tana who argues with Tana d'Vei Rebbi Yishmael is merely saying the Pashut Pshat.

4) Here are two more places where Rashi explains like the Tana who argues with Rebbi Yishmael:

a) Rashi in Shevuos 6b (DH Ho'il) writes that the verse, "He may not eat until he is pure," refers to "Azharas Kodesh" -- a warning against eating Korbanos before attaining purity. Tosfos (DH Lo) asks on Rashi that this does not follow either Rebbi Yochanan or Resh Lakish in Makos 14b. Tosfos adds that Rashi can be consistent with the Tana who argues with Rebbi Yishmael in Yevamos 75a.

I want to argue that the reason why Rashi explained according to this Shitah is that it follows the simple meaning of the verse, as the Tzelach that I cited above wrote -- that to explain that it refers to Terumah means uprooting the verse from its simple meaning. The way of Rashi is to explain according to the opinions that follow the Pashut Pshat, even if this is not according to the Halachic conclusion. (See Beis Yosef, OC 10, DH ul'Inyan, who writes that Rashi is a Mefaresh, not a Posek.)

b) Rashi (Kerisus 2a, DH v'Tamei she'Achal, in the right-hand column, 13 lines from the bottom of the page) writes that a Tamei person who ate Kodesh food transgresses a negative commandment derived from the verse "v'Lo Yochal Ad Asher Yit'har." This must be like the Tana who argues on Rebbi Yishmael since everyone else learns that it is referring to Terumah. Again, this Tana follows the Pashut Pshat, which is why Rashi chooses it.

5) The words of the Mizrachi that Rashi (in Chumash) always explains the verses according to the simple meaning:

a) I found that the chief commentator on Rashi on Chumash -- Rabeinu Eliyahu Mizrachi -- writes (on Rashi to Vayikra 5:10) that the practice of Rashi is always to explain the verses according to the simple meaning, not according to the Midrashim of Chazal, when these Midrashiom are far away from the Pshat in the verse. The Mizrachi writes also (on Rashi to Bamidbar 29:39) that when the Midrash is not consistent with the Pshat of the verse, Rashi leaves the Midrash and explains according to the simple meaning of the verse.

b) The Mizrachi is referring to the way of Rashi in his commentary on the Chumash, but if we assume that Rashi follows a similar policy in his commentary on Shas, then we can explain why, in Shevuos 6b and Kerisus 2a, as I wrote above, Rashi explains that "Ad Asher Yit'har" refers to eating Kodashim after bringing Kaparah. The Ritva and the Pnei Yehoshua on Shevous 6b, and the Cheshek Shlomo in Kerisus 2a, ask on Rashi why he explains according to the Tana who disagrees with Tana d'Vei Rebbi Yishmael. But now we can suggest an answer according to the Mizrachi, that Rashi is saying the simple Pshat.

Kol Tuv,

Dovid Bloom