Maharal (Gur Aryeh) says that “the Testimony” Moshe was commanded to put in the ark cannot mean the Luchos, as Moshe was told that G-d will be (future tense) giving him “the Testimony;” it therefore can’t refer to something that was already given to him. Since Rashi is of the opinion that the Mishkan wasn’t commanded until long after the sin of the golden calf (see his comments on 31:18), the first set of Luchos couldn’t be what Moshe was being told to put in the ark, as Moshe had shattered them upon seeing the golden calf. Besides, since they were shattered, they couldn’t be a “testimony” to anything. Moshe hewed the stone for the second Luchos and brought them to G-d (see 34:1), so it can’t be said that G-d gave those Luchos to Moshe either. Therefore, “the Testimony” that G-d “will give” to Moshe must refer to the Torah, which was given to him years later. In other words, included in the instructions to build the ark for the Mishkan was the commandment to (eventually) put the Torah into it. When the Mishkan was built, however, the Torah wasn’t written yet, so “the Testimony” must be referring to the Luchos.
There are several issues with Maharal’s approach. First and foremost, even if it explains how logistically each “Testimony” has to refer to what Rashi says it referred to, how could the same word (“Testimony”) used in the same context (building the Mishkan), in the same manner (what should be/was put in the ark) refer to two different things? The Torah uses the word “Luchos” numerous times; why use the same word that refers to “the Torah” instead of saying explicitly that it was the Luchos that were put in the ark? Additionally, Moshe providing the raw materials for the second Luchos doesn’t prevent his receiving the finished product from being described as “given to him.” Finally, I am not convinced that when Rashi says the commandment to build the Mishkan was given long after the sin of the golden calf he means the specifics described in 25:1-30:38 rather than the commandment to appoint Betzalel and Ahaliav and share the instructions with them (31:1-11). If so, the original instructions could have been given during the first set of 40 days Moshe spent on Mt Sinai, and “the Testimony that I will give you” could refer to the first Luchos. As a matter of fact, Midrash Lekach Tov, who also explains “the Testimony” Moshe was told to put in the ark as the Torah, says explicitly that the time frame for G-d giving it to him was “after 40 days.” Obviously, explaining “the Testimony” to be the Torah is not based on it being given to him years later.Midrash Lekach Tov’s approach raises difficulties as well. Like Rashi, he explains “the Testimony” that Moshe was commanded to put in the ark as the Torah, which is “forever a testimony that G-d chose [the Children of] Israel and gave them His Torah,” and “the Testimony” that was actually put in the ark as the Luchos. Yet, he applies the same verse (Mishlay 4:2, which explicitly refers to the Torah) to both. Why mention a verse that refers to the Torah if he really meant the Luchos, and/or why describe it as the Luchos if he really meant the Torah?
Maskil L’Dovid (25:16) says that when Rashi explains “the Testimony” as the Torah, he doesn’t mean the Torah scroll that Moshe wrote at the end of the 40 years in the desert, but the Luchos, as Rashi says explicitly when explaining what Moshe actually put in the ark. However, he doesn’t explain why Rashi calls it “the Torah” in one place and “the Luchos” in another. Additionally, as Maharal points out, when the Yerushalmi (Sh’kalim 6:1) discusses the dispute as to whether the Torah scroll was placed inside the ark or at its side, the commandment to put “the Testimony that I will give you” in the ark (25:16) is quoted as a proof-text, clearly indicating that this verse refers to the Torah scroll. [It should be noted, though, that Tosfos (HaShaleim 7) says it’s the word “es” that teaches us that the Torah scroll should also be put in the ark, so this verse being used as a proof-text doesn’t mean putting the Torah scroll in the ark decades later is the main focus of the verse.]
The Talmud (Shabbos 87a) says Moshe broke the Luchos based on G-d forbidding someone who did not maintain His covenant from participating in the Passover offering; if one commandment is off-limits for such a person, certainly the whole Torah should be. Putting aside what the logic of this argument is, some (see Torah Sh’laima 25:123) use this comparison (and other similar Midrashim) to suggest that the term “Luchos” refers to the whole Torah, and that Rashi means the same thing in both places. Besides sharing the same drawbacks as Maskil L’Dovid’s approach (including why Rashi uses different terms), basing the comparison on Moshe breaking the Luchos has an additional issue. The Luchos represented the covenant that was first being entered into, so breaking it represented the covenant not being in effect; this is not the same as saying the Luchos represented the commandments that result from the covenant being in effect. Moshe was preventing the commandments from applying to those who had rejected the covenant, he wasn’t nullifying the commandments themselves. It is therefore difficult to equate the Luchos with the Torah (as opposed to with the covenant necessary for the Torah to be given) based on how the Talmud explains why Moshe broke the Luchos.
Sh’mos Rabbah (33:1) uses a parable to explain why G-d commanded us to build the Mishkan, comparing the Torah to a king’s only daughter who married the king of another country. As difficult as it was to be separated from his beloved daughter, the king couldn’t tell her that she couldn’t leave. He therefore asked his new son-in-law to build small guest quarters for him, so that he can visit her anytime he wants. Similarly, G-d didn’t want to part with the Torah, but wanted us to have it, so asked us to build Him a dwelling place whereby He could still be near the Torah. Our connection with G-d comes through the Torah (“Yisroel v’Oraysa v’Kudsha B’rich Hu chad hu,” Israel and the Torah and the Holy One–blessed is He– are one), which was the centerpiece of the Mishkan. The Luchos may represent our covenant with G-d (“Luchos HaB’ris”), but they also represent G-d giving us the Torah (“Luchos HaEidus”), and contained (at the very least) the Ten Commandments.
The “Testimony” (“Eidus”) that was placed in the ark was put there because of it being “Torah,” the essence of our relationship with G-d. It “testified” that G-d chose us because He gave it to us (and only us). This is what Midrash Lekach Tov says explicitly, and what Rashi is saying as well (“that I commanded you the commandments that are written in it;” Rashi isn’t saying that the Torah proves it was G-d who gave us the commandments, but that G-d chose us by giving it to us and no one else). Therefore, whatever was considered “the Torah” was placed in the ark. By using the future tense (“that I will give you”), G-d included putting the Torah scroll, when it’s written, into the ark. At the time of the building of the Mishkan, though, the only thing tangible that was “Torah” were the Luchos, because they had “Torah” carved into them. Therefore, when Rashi explains what was physically put in the ark that was considered “Torah” (the “Testimony”), he tells us that it was the Luchos.