In Avoda Zara 12a, I mentioned Tosafos who says that the concept behind yotzei v'nichnas being effective is not that a spot check is good enough. Rather, the concept of יוצא ונכנס is that he creates fear on the goy who is constantly concerned that the mashgiach will show up unannounced and catch him red handed - נתפס עליו כגנב. Therefore, it is only effective in a situation where the goy has what to lose if he gets caught, and when there is a real concern that the mashgiach can and will show up an any moment.
The Cheshek Shlomo points out that the gemara in chulin 4a seems to echo this idea. The gemara says that according to Rava that yotzei v'nichnas is effective, why would the braisa speak about ישראל עומד על גביו, rather than speaking about the bigger chiddush of yotzei v'nichnas. The gemara explains - אמר לך יוצא ונכנס נמי כעובד על גביו דמי, meaning that it is the same. However, this doesn't seem to answer the gemara's question - it would still be a bigger chiddush to say that יוצא ונכנס works? The Cheshek Shlomo explains that the braisa is actually saying a big chiddush according to Rava. It is true that yotzei v'nichnas works, but one may think that it works as a spot check to allow us to assume that if now he didn't mess up now, he wouldn't have messed up at other times. By the braisa equating yotzei v'nichnas to ישראל עומד על גביו it is esentially teaching us that יוצא ונכנס works through the same method of someone being there constantly, since it creates a fear of someone walking in at any moment.
With this we can understand why Abaye disagreed with Rava and held that יוצא ונכנס doesn't work for shechita, even though it works everywhere else. The gemara seems to make a very superficial distinction between the case of the wine where the goy is in the store but not supposed to be touching it, and the case of shechita where he is actually touching it. Rashi 3b offers a deeper understanding to that distinction. Rashi explains that the reason shechita is different is that the animal is in his hand and כהרף עין שוהה או דורס - he can instantaneously with the twist of the wrist mess up the entire shechita. Since he can do so within a split second there is no longer the fear of getting caught which undermines the entire concept of יוצא ונכנס.