Having already instructed Moshe (in Pasuk 16) to place the Luchos inside the Aron, why does the Torah repeat it here?
Rashi: To teach us that the Luchos were to be placed in the Aron before the lid was placed on it, 1 as opposed to first putting on the lid and then removing it in order to place the Luchos inside. 2
Ramban: It is coming to explain the role of the Keruvim in the Mishkan - to form a Throne of Glory for Hashem, 3 whose Shechinah will descend to between the Keruvim, from which point He will communicate with Moshe. 4
Da'as Zekenim and Hadar Zekenim (both in Pasuk 16): Pasuk 16 is merely exlaining why one may not remove the staves, 5 whereas the current Pasuk presents the command to place them inside.
Rashash (in Yoma, 53): The Torah repeats it to teach us that the Luchos are crucial to the Aron and that, consequently, if the Luchos are missing, there is no point in placing the Aron in the Kodesh Kodshim. 6
Indeed that is what Betzalel did. See Pikudei, Sh'mos 40:20 (Rashi).
See Ramban's objection to this explanation. Moreover, in the earlier Pesukim, the Torah only mentioned the lid after instructing Moshe to place the Luchos inside the Aron, in which case the placing of the Luchos preceding that of the lid is self-evident?
Which explains why Hashem is called "Yoshev ha'Keruvim" - in Shmu'el 1, 4:4.
Like He did on Har Sinai (Refer also to 25:2:7:1), and similar to the Merkavah that Yechezkel saw by N'har K'var (See Yechezkel, 10:2).
Da'as Zekenim and Hadar Zekenim, Ibid.: Because it is very holy, since the Luchos will be placed into it.
Rashash (Ibid.): Which explains why they did not make an Aron for the second Beis-Hamikdash. See Oznayim la'Torah who elaborates.
