Tos attempts to explain the reason that moshuach milchama is disscused
before egla arufah. In his first answer he says since in the misnah of 32a
he was disscsing the appointment of a king he continued with egla arufa. This is quite difficult since the parsha of arufa is last. So what does tos. mean?
The way I understand Tosfos (42a DH Mashu'ach), he only suggests one answer for his question about the order of the Perakim. He explains that the Mishnah in Elu Ne'emarim (32a) which lists everything that is said in Lashon ha'Kodesh lists "Parshas Eglah Arufah" immediately after "Parshas ha'Melech" and before Mashu'ach Milchamah, while when the Mishnah goes on to explain the sources for all of these, it explains Mashu'ach Milchamah first (42a) and Eglah Arufah last (44b).
Tosfos' answer is that the Mishnah puts the words "Parshas Eglah Arufah" next to the words "Parshas ha'Melech" since they are both "Parshiyos," as opposed to Mashu'ach Milchamah which is not a " Parshas Mashu'ach Milchamah" (i.e. a simple Mitzvah of Keriyah, reading) but a Hasra'as Mashu'ach Milchamah, a warning and notfication to the troops about what to do -- see Meiri, who explains Tosfos' words as above. (Tosfos ha'Rosh gives another reason for putting Eglah Arufah first on 32a. His answer works even according to the Rashi 32a and the Bartenura who are Gores "Parshas Mashu'ach Milchamah," as Rebbi Akiva Eiger points out.)
However, when explaining them, the Mishnah explains Mashu'ach Milchamah first since it comes before the laws of Eglah Arufah in the end of Shoftim (Devarim 21) -- as you pointed out in your question.
Perhaps you want to know why the Mishnah only explains these two in the order in which they appear in the Torah, and not the rest of the laws in the Mishnah (such as Chalitzah and Berachos u'Kelalos, from Ki Savo, which are explained before Eglah Arufah and Mashu'ach Milchamah, from Shoftim). The answer appears to be that only these two appear in adjacent Parshiyos in the Torah.