How did Betzalel implement the command to overlay the Aron on the inside and outside with gold?
Rashi: He actually constructed three Aronos, the basic one of Atzei Shitim according to the Torah's specifications, one that fitted plush inside it and one into which the middle one fitted plush.
What was the "Zer Zahav"?
Rashi: The outer Aron (refer to 25:11:1:1) was higher than the other two to the extent that, even when the lid was placed inside it, it protruded slightly above it. 1
Rashi (in Tehilim, 139:3): "Zer" is a Mechitzah (a wall) that surrounds.
Targum Onkelos and Targum Yonasan: "Zer Zahav" is a golden crown.
Rashi in Eruvin, 4b explains that the Aron was nine Tefachim and the lid, one Tefach, in which case the outer golden Aron protruded a Tefach plus above the middle and inner Aronos - the 'plus' being the Zer Zahav'.
What was the significance of the Zer Zahav on the Aron?
Rashi: It symbolized the crown of Torah. 1
Da'as Zekenim and Moshav Zekenim: the crowns on the Mizbe'ach and on the Shulchan, which symoblized the crowns of Kehunah and Malchus, respectively, were taken by Aharon and David respectively. The crown of Torah, on the other hand, is open for anyone who wants to take it.
Seeing as there is no 'Yud' in the word "Zer", why is it proounced 'Zer' with a 'Tzeirei' and not 'Zar' with a 'Kamatz' or a 'Patach'?
Yoma, 72b: To teach us that if someone is meritous (by studying Torah with positive intentions), it will be a crown (a Zir) for him; whereas if not (in the event that he studies it with negative intentions, it will be estranged from him. 1
See Torah Temimah, note 17.
Why does the Torah write by the Aron "Ve'asisa "Alav Zer Zahav", and by the Shulchan "Ve'asisa Lo Zer Zahav"?
Ba'al ha'Turim (in Pasuk 10, citing the Midrash Rabah): Because the crown of Torah is greater than the other two crowns - of Malchus and Kehunah.
Seeing as the Aron was not seen on the inside, why did it need to be overlaid with gold also on the inside?
Yoma 72b: To teach us that a Talmid-Chacham whose inside is not like his outside is not a Talmid-Chacham. 1
Moshav Zekenim (in 37:1): In order to give Kavod to the Aron. This teaches us that one should honor the poor who learn Torah - just like they honored the wooden Aron due to the Torah that it contained.
Presumably, this is based on the fact that "Man is compared to the tree of the field" (Parshas Shoftim, 20:19) - symbolized by the wood that comprised the basic Aron.
Why did the Torah not command Moshe to make the Aron entirely of gold?
Da'as Zekenim: Because it would then have been too heavy to carry. Even though the Aron carried those who carried it, that was a temporary occurrence. 1 However, if so, why was Uza punished (for going to catch the Aron, if normally it did not carry itself)? This requires investigation. Similarly, the Mizbechos were of wood and only plated with gold and copper, lest they be too heavy.
Refer to 5:11:151:1 and note.
Moshav Zekenim (in 37:1): Because the Aron, which corresponded to the Kisei ha'Kavod above, 2 was of wood, because the Torah is called "Eitz Chayim". 3
And we do not rely on miracles. If so, how could the outer covering of the Aron, which was extremely thin (Maharsha, in Yoma 72b), and of gold (which is soft), bear the weight of the Luchos? They carried the Aron via staves in rings welded onto the covering! Perhaps super-refined gold is strong. Shlomoh ha'Melech made one Kikar of super-refined gold from a thousand Kikar of gold (Menachos 29a). However, the total donation of gold for the Mishkan was less than thirty Kikar (38:24), and much of it was used for the other Keilim and for plating the boards (PF).
As the Torah wrote in Beshalach, 15:17 "Machon le'Shivt'cha".
See Mishlei, 3:18.