On 3a, Rava asks on Abayey that Yotzei v'Nichnas is good l'chatchila regarding a goy touching wine, and therefore this would also apply to Shechitah. On 3b, the Gemara says that Abayey would respond hasam lo naga etc. Why couldn't Abayey give the following answers to Rava's question :
1) The wine has a chezkas kashrus, and we have a doubt if the goy made it assur, so in that case we can rely on Yotzei v'Nichnas l'chatchila, to assume nothing changed from its original Chazakah. But by Shechitah, the animal has a chezkas Isur from when it was alive, and we need to know that it became mutar through Shechitah, and for this we cannot rely on Yotzei v;nichnas l'chatchila, because it's not an issue of maintaining the previuos Chazakah, but of changing the Chazakah, and for that we need more certainty.
2) The wine case is a safek d'rabanan, because even if he touched it, this would render it stam yeinam, but it is not reasonable that he actually used it as yayin nesech, so maybe we can rely on yptzei v'Nichnas l'chatchila when it's only a safek d'rabanan, but by Shechitah it's a safek d'oraisa.
Yaron Barach, Brooklyn NY
Your 2 questions are strong ones and they are both asked by the Pnei Yehoshua.
(1)
(a) The Pnei Yehoshua answers that in fact originally Rava did not want to explain the Mishnah to refer to a scenario where the Yisrael is watching the Kusi slaughter, because he understood that this did not fit in well with the words of the Mishnah. This is because the end of the Mishnah 2a states that the Shechitah of everyone who slaughtered and was watched by others is Kosher. This implies that the Reisha of the Mishnah was not referring to a scenario where he was being watched.
(b) In addition Abaye made a convincing argument (below 4a) that Yotzei v'Nichnas is equivalent to
"Ba u'Metza'o" - that the Yisrael only came after he had slaughtered and found him.
(c) On the other hand, Rava maintained that in Sevara, being watched by a Yisrael is a strong logical reason to permit the Shechitah. This is because it is a "Milsa d'Avidi l'Igluyei" - if the Kusi should do something wrong with the Shechitah he is afraid of getting caught by the Yisrael who is walking in and out, and may give him a piece of meat to eat and prove that he did not slaughter well.
(d) In short, Rava maintained that logically one could rely on Yotzei v'Nichnas, but the problem is that this does not fit in with the words of the Mishnah. However once Rava found a Mishnah in Avodah Zara that Yotzei v'Nichnas is an acceptable Heter, then his reservations could be pushed aside, because he now had a source to rely upon. It is true that the wine is only an Isur d'Rabanan and that there is a Chezkas Heter, but since Rava understood that Yotzei v'Nichnas is a strong Sevara because the Kusi is afraid of getting caught, he was quite happy to rely on this Sevara even for a d'Oraisa with a Chezkas Heter. Rava now maintained that Abaye could not argue back to him that Yotzei v'Nichnas is equivalent to Ba u'Metza'o, because Rava had a Mishnah in Avodah Zara which showed otherwise.
(2) The Rashash answers that your Chiluk between d'Oraisa and d'Rabanan is actually hinted at by the Gemara when it answers that it is only b'Di'eved that we really on the Shomer for the wine. One can only distinguish between b'Di'eved and Lechatchilah in d'Rabanan prohibitions, not for d'Oraisas.
(3) I also found in the Teshuvas Mahari Asad (a great Talmid of the Chasam Sofer) YD end #135, who answers on the basis of the Ran (Avodah Zara top 13b in Rif pages) in the name of the Ra'avad that for food forbidden because of contact with Nochri, one forbids it even if there is no taste of the Isur present. Chazal were more stringent on this so that people should not break down the barriers. Just as one cannot rely on there being no taste discernible, so also for these Halachos one cannot rely on a Rov. If so one cannot also not rely on Chazakah because Kidushin 80a states that Rov is stronger than Chazakah. Since one cannot rely on Chazakah it should not help us that the wine has a Chezkas Heter but since we see that Yotzei v'Nichnas helps for the wine then it should also help for Shechitah even though there is a Chezkas Isur.
Even though I have cited some of the answers of the Acharonim to your questions I still think there may be room for further thought on this Sugya but anyway that is all for the time-being.
Kol Tuv,
Dovid Bloom