Kli Yakar explains that the verse distinguishes between the priest who eats the meal offering and the matzah eaten: the priest eats his portion beside the altar’s portion to signify its atoning function, while the matzah requires a holy place because its freedom from leaven gives it an aspect of holiness.
מַצּוֹת תֵּאָכֵל בְּמָקוֹם קָדוֹשׁ בַּחֲצַר אֹהֶל מוֹעֵד יֹאכְלוּהָ. פֵּרֵשׁ רַשִׁ״י בְּמָקוֹם קָדוֹשׁ, וְאֵיזֶהוּ – בַּחֲצַר אֹהֶל מוֹעֵד. וּמִכָּל מָקוֹם ״בְּמָקוֹם קָדוֹשׁ״ מְיֻתָּר, גַּם ״תֵּאָכֵל״ ״יֹאכְלוּהָ״ אֶחָד מֵהֶם מְיֻתָּר, וּמַשְׁמָעוּת הַלָּשׁוֹן הוּא שֶׁיֵּשׁ כָּאן בְּחִינַת הָאוֹכֵל וְהַנֶּאֱכָל. בְּחִינַת הָאוֹכֵל, הַיְינוּ שֶׁהַכֹּהֵן הָאוֹכֵל אוֹתָהּ צָרִיךְ שֶׁיֵּדַע שֶׁאֲכִילָתוֹ מִשֻּׁלְחַן גָּבוֹהַּ הִיא, וּמִן הַדִּין שֶׁתִּהְיֶה הַמִּנְחָה כָּלִיל לַגָּבוֹהַּ זוּלַת שֶׁהַקָּדוֹשׁ בָּרוּךְ הוּא נָתַן לוֹ חֶלְקוֹ מֵאִשָּׁיו, וְאִם כֵּן צָרִיךְ הַכֹּהֵן לֶאֱכוֹל חֶלְקוֹ בַּמָּקוֹם שֶׁנֶּאֱכָל חֵלֶק גָּבוֹהַּ, דְּהַיְינוּ בַּחֲצַר אֹהֶל מוֹעֵד כִּי שָׁם מְקוֹם הַמִּזְבֵּחַ, וְאַף עַל פִּי שֶׁבֶּאֱמֶת הַמָּקוֹם הַהוּא קָדוֹשׁ, מִכָּל מָקוֹם אֵין קְפֵידָא עַל הָאוֹכֵל מִצַּד קְדֻשַּׁת הַמָּקוֹם כִּי אִם מִצַּד שֶׁצָּרִיךְ לְהַסְמִיךְ אֲכִילָתוֹ אֶל אֲכִילַת הַמִּזְבֵּחַ, לְהוֹרוֹת שֶׁכְּמוֹ שֶׁאֲכִילַת הַמִּזְבֵּחַ מְכַפֶּרֶת כָּךְ אֲכִילַת הַכֹּהֲנִים, הַבְּעָלִים מִתְכַפְּרִין בָּהֶם. אָמְנָם בְּחִינַת הַנֶּאֱכֶלֶת הִיא הַמַּצָּה, מִצַּד הֱיוֹתָהּ נְקִיָּה מִן הַשְּׂאוֹר יֵשׁ בַּמַּצָּה צַד קְדֻשָּׁה, עַל כֵּן נֶאֱמַר ״מַצּוֹת תֵּאָכֵל בְּמָקוֹם קָדוֹשׁ״, כִּי מִצַּד בְּחִינַת הַמַּצָּה יֵשׁ קְפֵידָא שֶׁיִּהְיֶה הַמָּקוֹם קָדוֹשׁ. וְאַחַר כָּךְ נָתַן טַעַם עַל שְׁנֵיהֶם, כִּי עַל מַה שֶּׁכָּתַב ״בַּחֲצַר אֹהֶל מוֹעֵד יֹאכְלוּהָ״, זֶהוּ לְפִי שֶׁ״חֶלְקָם נָתַתִּי אֹתָהּ מֵאִשָּׁי״, עַל כֵּן צְרִיכִין שְׁנֵיהֶם לִהְיוֹת בִּמְחִצָּה אַחַת. וְעַל מַה שֶּׁכָּתַב ״מַצּוֹת תֵּאָכֵל בְּמָקוֹם קָדוֹשׁ״, נָתַן טַעַם וְאָמַר ״קֹדֶשׁ קָדָשִׁים הִיא כַּחַטָּאת וְכָאָשָׁם״, כִּי הַחַטָּאת וְהָאָשָׁם הַבָּאִים עַל כַּפָּרַת הַחֵטְא נִקְרְאוּ קֹדֶשׁ קָדָשִׁים, כִּי הַצַּדִּיק גָּמוּר שֶׁלֹּא חָטָא כְּלָל קָדוֹשׁ הוּא לַה׳, אֲבָל הַחוֹטֵא וְשָׁב בִּתְשׁוּבָה הוּא קֹדֶשׁ קָדָשִׁים, כִּי בְּמָקוֹם שֶׁבַּעֲלֵי תְּשׁוּבָה עוֹמְדִים אֵין צַדִּיקִים גְּמוּרִים יְכוֹלִים לַעֲמוֹד בּוֹ (ברכות לד:), וְרז״ל אָמְרוּ (יומא פו:) שֶׁהָעוֹשֶׂה תְּשׁוּבָה מֵאַהֲבָה הַזְּדוֹנוֹת נַעֲשִׂין לוֹ כִּזְכֻיּוֹת, כְּמוֹ שֶׁיִּתְבָּאֵר בְּעֶזְרַת ה׳ לְקַמָּן פָּרָשַׁת וַיֵּלֶךְ. וְזֶה מַדְרֵגָה גְּדוֹלָה שֶׁאֵינָהּ בְּצַדִּיק גָּמוּר, מִלְּבַד שְׁאָר מַעֲלוֹת שֶׁזָּכְרוּ רז״ל שָׁם, עַל כֵּן דִּין הוּא שֶׁתִּהְיֶה הַחַטָּאת קֹדֶשׁ קָדָשִׁים. וְכֵן הַמַּצָּה צְרִיכָה מָקוֹם קָדוֹשׁ מִזֶּה הַטַּעַם, כִּי גַּם הִיא קֹדֶשׁ קָדָשִׁים מִצַּד הַרְחָקַת הַשְּׂאוֹר שֶׁבָּעִסָּה הַמְחַלֵּל קְדֻשַּׁת הָאָדָם.
It shall be eaten unleavened in a holy place, in the court of the Tent of Meeting they shall eat it. Rashi explains it as, in a holy place — and what is it? In the court of the Tent of Meeting.“ Nevertheless, in a holy place is redundant, and also shall be eaten and they shall eat it — one of them is redundant. The meaning of the language suggests that there are two aspects here: the eater and what is eaten. The aspect of the eater means that the priest who eats it needs to know that his eating is from the Divine table, and by law, the meal offering should be entirely consumed by the altar, except that the Holy One, blessed be He, gave him his portion from His offerings. Therefore, the priest needs to eat his portion in the place where the Divine portion is consumed, namely in the court of the Tent of Meeting, because that is where the altar is located. And even though that place is indeed holy, the requirement for the eater is not because of the holiness of the place, but rather because he needs to connect his eating to the consumption by the altar, to indicate that just as the consumption by the altar atones, so too does the eating by the priests — the owners receive atonement through them. However, the aspect that is eaten is the matzah. Due to its being clean from leaven, there is an aspect of holiness in matzah. Therefore, it says unleavened bread shall be eaten in a holy place, because from the perspective of the matzah’s quality, there is a requirement that the place be holy. And afterward, it gave a reason for both: Regarding what it said in the courtyard of the Tent of Meeting they shall eat it, this is because I have given it as their portion from My fire-offerings. Therefore, both need to be within the same partition. And regarding what it said, unleavened bread shall be eaten in a holy place, it gave the reason saying it is most holy, like the sin offering and like the guilt offering. For the sin offering and guilt offering that come for atonement of sin are called most holy, because the completely righteous person who has not sinned at all is holy to the Lord, but the sinner who returns in repentance is most holy, for in the place where penitents stand, even the completely righteous cannot stand (Berakhot 34b). And our Sages said (Yoma 86b) that one who repents out of love, his intentional sins are transformed into merits, as will be explained, God willing, later in the portion of Vayelech. And this is a great level that is not found in the completely righteous person, besides the other virtues that our Sages mentioned there. Therefore, it is proper that the sin offering be most holy, and similarly, the matzah requires a holy place for this reason, because it too is most holy due to the removal of the leaven in the dough which profanes a person’s holiness.