The question is why Mishna 1 doen't apply and how can Leah come back to Baruch according to Rabbi Yose. To find the answer, we need to add one statement in quotation of Mishna 1 and 3.
וצריכה גט מזה ומזה
Leah needs a get from Aharon and from Baruch.
ר' יוסי אומר כל שפוסל ע"י אחרים פוסל ע"י עצמו
וכל שאין פוסל ע"י אחרים אינו פוסל ע"י עצמו
רבי יצחק נפחא אמר לעולם אסיפא
Rav Yitschack Nafcha says that the second statement of Rabbi Yose, which is lenient comparatively to Tana Kama opinion, says that when Leah can come back to Baruch, so, indeed, Myriam can come back to Aharon. And the case in which Leah can come back to Baruch doesn't exist according to Tana Kama. Because Tana Kama holds that the prohibition for Leah to marry back Baruch is simply a Knas because she didn't verify enough her husband death. But for Rabbi Yose, there is no such Knas. The only problem is when it's shows as Baruch takes back his divorced and remarried and divorced wife. And when Leah was obviously in the hallachic impossibility to be married to Aharon, everybody knows that the relationship between Leah and Aharon wasn't marrital. It was an involuntary biat znut. Since we assume that Baruch is not Cohen, Leah will come back to Baruch. Aharon doesn't give her a Get. Therefore, Myriam doesn't seem to be the sister of his divorced Leah. He is allowed to come back to Myriam.
The reason is that Rabbi Yose disagrees with Tana Kama (1) regarding the rational of Mishna 1. According to Rabbi Yose in Mishna 1 the reason for the prohibition for Leah to come back to Baruch is that people may think that she divorced and afterwards married another man and next married a second time Baruch. And we need to make clear that it's prohibited.
In our case, marriage doesn't match between Leah and Aharon, because she is the sister of his wife. Now people see that Myriam is alive and understand that marriage between Aharon and Leah was nothing. So, Aharon will not give a Get to Leah. And people will not think that Leah comes back to Baruch through a second marriage after she divorced her second husband. So Mishna 1 is not a contradiction to the Din of Rabbi Yose.
Source of this answer is Rashi 95b.
לעולם אסיפא... ... וקא"ל רבי יוסי אשתו דליכא למימר תנאה הואי ליה - להאי באשתו ראשונה וכ"ע ידעי דנשואי שניה טעות הן ולא אתי למימר גירשה בעלה ונשאה זה Rabbi Yose is teaching a leniency, in his last sentence. because he (Aharon) married his first wife (Myriam), in a way which cannot lead to believe that there was an unfulfilled condition. (Because this marriage was followed by an intercourse and a man is not suspected to make a non marrital intercourse, called biat znut)
and a marriage invo. Since his first wife (Myriam) is undoubtedly his wife, everybody knows that the marriage with the second wife (Leah) was only an error.
דהא אפילו גירשה בעלה אסורה להאי ומידע ידעי דסהדי אטעינהו אינו פוסל ע"י גיסו כשאר אשה הנשאת בעד אחד דהתם הוא דאתי למימר גירש זה כו' ואי מחזיר אמרי זה מחזיר גרושתו מן הנשואין Even if we would believe that Baruch divorced Leah, the prohibition of Leah towards Aharon doesn't change. Therefore, when people see that both sisters Myriam and Leah are alive together, they know that the marriage between Aharon and Leah was erroneous and not valid.
Remember that it's impossible to marry the sister of his own divorced wife. There is in this case a leniency which is not possible in the standard case. The standard case is the case in which Leah married a man who have nothing to do with Myriam. And if Leah is divorced from Baruch, the marriage with the man matches. So, if Baruch comes back to Myriam, this looks as if he takes back his divorced woman after her second marriage with another man.
אבל הכא לא הלכך אין פוסל נמי על ידי עצמו Since this case is not similar to the standard case, and Aharon can take back Myriam.
אבל היכא דהואי קמייתא ארוסתו דאיכא למימר תנאה הוה ליה בקדושין סברי אינשי דנשואי שניה נשואין גמורין ואמרי גירשה בעלה ונשאה זה But if Myriam was only mekuddeshet, people will say that the Kiddushin were conditioned. So the true marriage of Aharon is with Leah. People will say that Baruch divorced Leah and she further married Aharon
ואי משום אחות אשה תנאה הוה לו בקדושי ראשונה ולא נתקיים
ואי הדרא אשת גיסו לבעלה אמרי אינשי מותר להחזיר גרושתו משניסת הלכך הוא פוסל על ידי אחרים והואיל ואהנו מעשיו פוסל נמי ע"י עצמו Leah cannot go back to Baruch because people will say he returned his divorced after she divorced from a second marriage and people would believe that there is no problem to remarry his first wife if she divorced from her second husband.
ולתנא קמא טעמא דהניסת בעד אחד אסורה לחזור לאו משום שמא יאמרו זה מחזיר גרושתו משנשאת אלא משום דקנסוה רבנן משום דלא דייקא שפיר הלכך כל מאן דנסבה פסל לה אקמא: But according to Tana Kama Leah is always prohibited for Baruch because chachamim punished her as if she did cheat her husband intentionally. (This point, to regard him as she didn't make a sufficient effort to check that her husband died is discussed in folio 92a, and there, Rashi explaining Rav Nachman, is congruent to his words here)