Why were the Leviim the ones commanded to place the Sefer Torah next to/or inside the Aron? While it may be true that a Yisrael was not permitted entry into the Kodesh HaKodoshim, Holy of Holies, where the Aron was situated, neither were the Kohanim and Leviim permitted entry. Indeed, the only one who was allowed into the Kodesh HaKodoshim was the Kohen Gadol on Yom Kippur. Otherwise, it was off-limits to everyone. As such, why were the Leviim singled out? Obviously, this was a one-time dispensation. If so, our question still stands. Why was Shevet Levi chosen above anyone else?
The Brisker Rav, zl, cites the Rambam in his preface to Seder Zeraim, and also in his preface to the Yad Hachazakah, that Moshe Rabbeinu actually wrote thirteen Sifrei Torah and gave one to each tribe. He gave the thirteenth scroll to Shevet Levi. He then told them, “Take this scroll and place it in the Aron.” The question is obvious: What about Efraim and Menashe, who were the two Shevatim that comprised Yosef’s Shevet? If so, he should have written fourteen scrolls – thirteen for the tribes and one for the Aron. We must posit, explains the Brisker Rav, that he wrote fourteen Sifrei Torah, but one of them, the scroll belonging to Shevet Levi, was placed in the Aron. This is why Shevet Levi was charged with placing the scroll in the Aron; after all, it was their Sefer Torah.
We now understand Rashi’s explanation concerning the nation’s complaint regarding the choice of Shevet Levi receiving a Torah. What was their problem? Everyone, each of the tribes, received a Torah from Moshe. We must say that they each took umbrage with Shevet Levi’s sefer Torah – and not theirs – being selected to be housed in the Kodesh HaKodoshim next to/inside the Aron. It was this Torah that remained pristine – never leaving the Sanctuary’s environs. Thus, when a question arose concerning a Tribal Torah scroll, such as spelling, etc., it was checked against the scroll that remained in a pristine environment.