1)
Why did the Torah not instruct Moshe to place the Luchos inside the Aron?
1.
Ramban: Because, by referring to the Aron as "Aron ha'Eidus" (with reference to the Luchos), this was self-understood. 1
1
Moreover, Hashem had already told Moshe in Terumah, 25:21 that he would "place the lid on the Aron and put the Luchos inside it" (Ramban).
2)
Since when did the Paroches cover the Aron?