The gemara says that the Chidush of the Itzteva is that we say Dofen Akumah from all four sides. This implies that the Mishnah which discusses a roof with a hole in (which does not teach this Halachah) is talking about a hole that is close to one of the sides and therefore it doesn't involve Dofen Akumah from all four sides. That is why we don't see that Dofen Akumah applies from all four sides from that Mishnah.
Why then does Rashi earlier on the Amud explain that the hole (in the case of the Mishnah) is in the center of the roof? In fact, Rashi on that Mishnah itself (17a) says even more explicitly that the hole is at a distance from all four of the walls!
Allow me to give a brief overview of the Gemara, which I believe will answer your question. The Gemara gives three cases, and explains the teaching of each one. The novelty of the case of the house is that we say Dofen Akumah on all four sides. The Gemara explains that the novelty of the case of "Itzteva Min ha'Tzad" -- "a platform on the side" is that we can say Dofen Akumah even in case where we do not have a regular Kosher wall (as the wall is more than twenty Amos tall, see Rashi DH "Hasam Hu"). The Gemara then asks, why do we need the case of "Itzteva b'Emtza" -- "a platform in the middle?" The Gemara answers that we do not yet know that we apply the teaching learned by Itzteva Min ha'Tzad to a case where all three irregular walls require Dofen Akumah. This is taught by the case of Itzteva b'Emtza.
Kesivah v'Chasimah Tovah,