What you are really asking is how is the term Rakia (רקיע) understood when used in the Torah?
The best way to understand Rakia in English is to think of what is called a phase separation in chemistry.
Phase separation is the creation of two distinct phases from a single homogeneous mixture. The transition point between the two distinct phases is the Phase Separation which in Hebrew is called רקיע.
To really grasp the ramifications of the idea of Phase Separation requires looking at the ideas of Colloid, Mixture, Solution and Suspension as they apply in chemistry.
In terms of the Creation of the universe, the two distinct phases are the spiritual domain, meaning the domain of Angels (אלקות) and the physical, material domain (גשמיות), meaning stars, constellations and planets of this world (עולם הזה). This is referred to as Yesh (יש), Being.
But it is important to note that the two distinct phases actually originate and arise from one, single, homogeneous state, G-d at His essence (מהות), meaning אין סוף. This is often referred to as Creation Ex-Nihilo (יש מאין)
The point of phase separation itself, meaning the Rakia, is apart from either of the two distinct phases and is equated with the geometric concepts of point (נקודה), line (קו) and field (שטח). Each of these three concepts are associated with greater or lesser states of non-existence or nullification (ביטול היש).
In the context of your Mishnah, it is addressing the condition and effect of one of the two distinct phases, meaning Tumah as it pertains to the physical, material state (יש). But the Rakia itself is above the distinct phases and in fact, transcends that state of being altogether (ביטול היש היינו אין).
In truth, to better understand this requires careful reflection upon Bereshit 1:6-10.
וַיֹּ֣אמֶר אֱלֹהִ֔ים יְהִ֥י רָקִ֖יעַ בְּת֣וֹךְ הַמָּ֑יִם וִיהִ֣י מַבְדִּ֔יל בֵּ֥ין מַ֖יִם לָמָֽיִם׃
וַיַּ֣עַשׂ אֱלֹהִים֮ אֶת־הָרָקִ֒יעַ֒ וַיַּבְדֵּ֗ל בֵּ֤ין הַמַּ֙יִם֙ אֲשֶׁר֙ מִתַּ֣חַת לָרָקִ֔יעַ וּבֵ֣ין הַמַּ֔יִם אֲשֶׁ֖ר מֵעַ֣ל לָרָקִ֑יעַ וַֽיְהִי־כֵֽן׃
וַיִּקְרָ֧א אֱלֹהִ֛ים לָֽרָקִ֖יעַ שָׁמָ֑יִם וַֽיְהִי־עֶ֥רֶב וַֽיְהִי־בֹ֖קֶר י֥וֹם שֵׁנִֽי׃ {פ}
וַיֹּ֣אמֶר אֱלֹהִ֗ים יִקָּו֨וּ הַמַּ֜יִם מִתַּ֤חַת הַשָּׁמַ֙יִם֙ אֶל־מָק֣וֹם אֶחָ֔ד וְתֵרָאֶ֖ה הַיַּבָּשָׁ֑ה וַֽיְהִי־כֵֽן׃
וַיִּקְרָ֨א אֱלֹהִ֤ים ׀ לַיַּבָּשָׁה֙ אֶ֔רֶץ וּלְמִקְוֵ֥ה הַמַּ֖יִם קָרָ֣א יַמִּ֑ים וַיַּ֥רְא אֱלֹהִ֖ים כִּי־טֽוֹב׃
That Mayim (מים) is alluding to the concept of Tzaddik (צדיק), that Mayim is the gematria value of the letter (צ) Tzadi(k). צדיק יסוד עולם
Water was at the beginning one, which through the paradigm of Creation will manifest within the universe as two, like it states in Bereshit 1:2,
וְהָאָ֗רֶץ הָיְתָ֥ה תֹ֙הוּ֙ וָבֹ֔הוּ וְחֹ֖שֶׁךְ עַל־פְּנֵ֣י תְה֑וֹם וְר֣וּחַ אֱלֹהִ֔ים מְרַחֶ֖פֶת עַל־פְּנֵ֥י הַמָּֽיִם׃
that the Ruach Elokim refers to Moshiach as a single individual like is stated in the commentary of the Tur, (in the example of Moshe Rabbeinu,(the paradigm of the first and final Redeemer) combining both the qualities of Moshiach ben Yosef and Moshiach ben David. That Moshe is spread throughout each and every generation (like the word רקיע connotes spreading), like it states in Tikkunei Zohar 112a:13)
וְאִתְפַּשְׁטוּתֵיהּ דְּמשֶׁה בְּכָל דָּרָא וְדָרָא וּבְכָל צַדִּיק וְצַדִּיק
This is alluded to by the expression, על-פני המים. That על-פני is referring to the פנימיות, the inner letters of the word צדיק, meaning ד״ויד-י״וסף. That single individual, that single צדיק is then separated into two distinct phases like it states in Bereshit 1:6-7.
That Upper Water is referring to Tzaddik Elyon (צדיק עליון) meaning (צדיק צלמו), the aspect of Yesod of Nukvah (יסוד דנקבה). That עליון is gematria צלמו. This refers to Moshiach ben David (משיח בן דויד).
So too, Lower Water (המים מתחת) is referring to Tzaddik Tachton (צדיק תחתון), meaning (צדיק יהוה), the aspect of Yesod of Zachar or Ze'ir Anpin (יסוד דזכר). This is Moshiach ben Yosef (משיח בן יוסף).
When the two separate and distinct personalities of Moshiach ben David and Moshiach ben Yosef are merged together as a single individual, then Tumah is no longer relevant to Moshiach. This is in keeping with the statement from Zechariah 23:2 which says:
וְהָיָה֩ בַיּ֨וֹם הַה֜וּא נְאֻ֣ם ׀ יְהֹוָ֣ה צְבָא֗וֹת אַכְרִ֞ית אֶת־שְׁמ֤וֹת הָֽעֲצַבִּים֙ מִן־הָאָ֔רֶץ וְלֹ֥א יִזָּכְר֖וּ ע֑וֹד וְגַ֧ם אֶת־הַנְּבִיאִ֛ים וְאֶת־ר֥וּחַ הַטֻּמְאָ֖ה אַעֲבִ֥יר מִן־הָאָֽרֶץ׃
This is referred to as עולם התחיה, the later stage of the Days of Moshiach. This is the resurrected Moshiach referred to in Yechezkel 37:15-19 and also tractate Sukkah 52b.
וַיְהִ֥י דְבַר־יְהֹוָ֖ה אֵלַ֥י לֵאמֹֽר׃
וְאַתָּ֣ה בֶן־אָדָ֗ם קַח־לְךָ֙ עֵ֣ץ אֶחָ֔ד וּכְתֹ֤ב עָלָיו֙ לִֽיהוּדָ֔ה וְלִבְנֵ֥י יִשְׂרָאֵ֖ל חֲבֵרָ֑ו וּלְקַח֙ עֵ֣ץ אֶחָ֔ד וּכְת֣וֹב עָלָ֗יו לְיוֹסֵף֙ עֵ֣ץ אֶפְרַ֔יִם וְכׇל־בֵּ֥ית יִשְׂרָאֵ֖ל חֲבֵרָֽו׃
וְקָרַ֨ב אֹתָ֜ם אֶחָ֧ד אֶל־אֶחָ֛ד לְךָ֖ לְעֵ֣ץ אֶחָ֑ד וְהָי֥וּ לַאֲחָדִ֖ים בְּיָדֶֽךָ׃
וְכַֽאֲשֶׁר֙ יֹאמְר֣וּ אֵלֶ֔יךָ בְּנֵ֥י עַמְּךָ֖ לֵאמֹ֑ר הֲלֽוֹא־תַגִּ֥יד לָ֖נוּ מָה־אֵ֥לֶּה לָּֽךְ׃
דַּבֵּ֣ר אֲלֵהֶ֗ם כֹּה־אָמַר֮ אֲדֹנָ֣י יֱהֹוִה֒ הִנֵּה֩ אֲנִ֨י לֹקֵ֜חַ אֶת־עֵ֤ץ יוֹסֵף֙ אֲשֶׁ֣ר בְּיַד־אֶפְרַ֔יִם וְשִׁבְטֵ֥י יִשְׂרָאֵ֖ל חֲבֵרָ֑ו וְנָתַתִּי֩ אוֹתָ֨ם עָלָ֜יו אֶת־עֵ֣ץ יְהוּדָ֗ה וַֽעֲשִׂיתִם֙ לְעֵ֣ץ אֶחָ֔ד וְהָי֥וּ אֶחָ֖ד בְּיָדִֽי׃
That G-d, at His essence (מהות), transcends letters and names altogether. But as part of Creation, G-d dressed, so to speak within His names. This is the meaning of the opening lines of the Adon Olam prayer.
אֲדוֹן עוֹלָם אֲשֶׁר מָלַךְ, בְּטֶֽרֶם כָּל יְצִיר נִבְרָא:
לְעֵת נַעֲשָׂה בְחֶפְצוֹ כֹּל, אֲזַי מֶֽלֶךְ שְׁמוֹ נִקְרָא:
וְאַחֲרֵי כִּכְלוֹת הַכֹּל, לְבַדּוֹ יִמְלֹךְ נוֹרָא:
וְהוּא הָיָה וְהוּא הֹוֶה, וְהוּא יִהְיֶה בְּתִפְאָרָה:
וְהוּא אֶחָד וְאֵין שֵׁנִי, לְהַמְשִׁיל לוֹ לְהַחְבִּֽירָה:
