Why did Moshe see fit to mention the manufacture of the second Luchos?
Ramban and Seforno: To teach us that, in spite of all Moshe's efforts to obtain atonement, so great was the sin of the Eigel ha'Zahav that, although the second Luchos were once again written by Hakadosh-Baruch-Hu, they were manufactured by Moshe, since the people were no longer worthy of Luchos that were Divinely made. 1
What is the significance of the Aron Eitz that Moshe was told to manufacture?
Rashi and Ramban #1: It was a purely wooden Aron with a wooden lid that was to house the second Luchos (and the broken ones
Rashi: In fact, this Aron subsequently accompanied them when they went to war, and on the one occasion that the main Aron was taken to the battle-front, they were punished and the P'lishtim captured it. See Ramban's objection to this explanation. According to him, Moshe's Aron was hidden once the Luchos were transferred to the Aron that Betzalel made.
Ramban: In fact, the command to make the Aron is synonymous with the command to build the Mishkan (which preceded the sin of the Golden Calf
If Hashem instructed Moshe to make a wooden Aron after ascending Har Sinai the third time with the second set of Luchos, where did he place the Luchos upon his return?
Ramban #1: Hashem meant that he should make a wooden Aron now, in which to place the Luchos when he returned from Har Sinai.
Because even though the instructions to build the Aron are mentioned last, it does not mean that he should make it last.
Rashi: This cannot have been the Aron that Betzalel made, since they did not begin building the Mishkan until after Moshe descended with the Luchos on Yom Kipur, and even then, Betzalel first built the Mishkan, and the Aron and the other Keilim only afterwards.
Ramban: Which is where the broken Luchos were already lying.