וַיִּקַּ֞ח וַיִּתֵּ֤ן אֶת־הָעֵדֻת֙ אֶל־הָ֣אָרֹ֔ן וַיָּ֥שֶׂם אֶת־הַבַּדִּ֖ים עַל־הָאָרֹ֑ן וַיִּתֵּ֧ן אֶת־הַכַּפֹּ֛רֶת עַל־הָאָרֹ֖ן מִלְמָֽעְלָה׃
Lalu ia mengambil loh-loh kesaksian dan memasukkannya ke dalam tabut, lalu memasang kayu-kayu pengusung pada tabut itu, dan meletakkan tutup tabut di atas tabut itu.
Siftei Chakhamim
The Torah, which is testimony. . . [Question:] It is written in 40:20, “He took the Testimony and placed it into the ark,” and Rashi explains it means the Tablets. Furthermore, the Torah was not written until the end of the forty years. [Why then does Rashi here say that “Testimony” means the Torah?] It seems the answer is: In our verse it is written, “The Testimony that I will give you,” in the future tense. But, the Ten Commandments were already given! Although the Tablets were broken, Moshe assumedly wrote it down or he prayed that the Tablets be restored to their original form. Perforce, our verse refers to the entire Torah, which would be written later.
Rashi
ואל הארן תתן את העדות AND IN THE ARK THOU SHALT PUT THE TESTIMONY — I do not know why this is repeated for it has already been commanded, (v. 16) “and thou shalt put the Testimony in the ark”. One may say that it intends to tell us that whilst the ark is still by itself — i. e. without the cover — he should first put the Testimony into it, and only afterwards should he put the cover on it for the first time. Thus indeed do we find: that when he (Moses) erected the Tabernacle it is stated, (Exodus 40:20) “and he [took and] put the Testimony into the ark”, and afterwards it says, “and he put the cover upon the ark above it” (cf. Talmud Yerushalmi Shekalim 6:1).
Or HaChaim
ונתת את הכפרת על הארון מלמעלה, "And you shall put the lid on top of the ark, from above;" Why did the Torah have to repeat that the "testimony" (Tablets with the Ten Commandments) should be placed inside the ark? We have already been told of this in 25,16! Rashi answers this problem saying that Moses was to first put the Tablets inside and subsequently to put the lid on the ark. He quotes 40,20 where the Torah describes Moses carrying out the instructions given here. Rashi's commentary suggests that unless the Torah had repeated itself one could have erred and thought that the Tablets were to be placed on top of the lid of the ark. I am not satisfied with this. First of all, there was no room on top of the lid for the Tablets as the whole top of the lid was taken up by the cherubs. Besides, if the Torah was concerned about the reader making such an error, it only had to add the word בתוך, "inside," in verse 16 instead of writing אל! There are other objections that could be raised against Rashi's commentary. The comments by Rabbi Eliyah Mizrachi on this duplication are not compatible with his usually profound insights. He wanted to defend Rashi by using the fact that Rabbi Avraham ibn Ezra did not see any need to comment as proof that there is no difficulty at all. With all due respect, I feel that Rabbi Mizrachi succeeded in defending Rabbi Ibn Ezra's words rather than those of Rashi. The instructions in verse 16 had to precede those in verse 21 as otherwise the Torah would have commanded placing the lid on an empty ark, seeing that the instruction to put the Tablets inside it would have been issued after the directive to put the lid on top of the ark!
Rashi
ויעל עליו וגו׳ AND OFFERED UPON IT etc. Not only during the first seven days of the consecration of Aaron and his sons during which Moses set the dwelling up and then dismantled it, but also on the eighth day of the consecration which was the day of the final erection of the dwelling for its ordinary purposes did Moses officiate and offer the congregational sacrifices except those which had been commanded exclusively for that very day, as it is said, (Leviticus 9:7) “[And Moses said to Aaron], approach unto the altar and offer etc.