Rashi does not explicitly mention the small Alef, but rather simply focuses on the difference between Vayikra and Vayikar, which is how the word would read without the Alef altogether. Much has been said about the fact that the small Alef would represent Moshe's humility, and that by making the Alef small, Moshe would be therefore giving less emphasis to the fact that G-d called out to him.
The fact that Alef is singled out and made smaller, however, suggests that Moshe is not at all trying to make himself appear more like Bilaam. On the contrary, he is emphasizing the difference between himself and Bilaam, which is exactly what Rashi picks up on. What is that difference? Humility.
19. Whoever possesses the following three traits is of the disciples of our father Abraham; and whoever possesses the opposite three traits is of the disciples of the wicked Balaam. The disciples of our father Abraham have a good eye (Ayin), a meek spirit (Ruach) and a humble soul (Nefesh). The disciples of the wicked Balaam have an evil eye, a haughty spirit and a gross soul. (Pirkei Avot, Chapter 5)
In Ecclesiastes (Kohelet), King Solomon states that the difference between a man and an animal is Ayin (nothing). It's not that there is no difference, but that the difference is the ability to be "nothing," a humble vessel.
|19. For there is a happening for the children of men, and there is a happening for the beasts-and they have one happening-like the death of this one is the death of that one, and all have one spirit, and the superiority of man over beast is nought [Ayin, with an Alef], for all is vanity.||יט. כִּי מִקְרֶה בְנֵי הָאָדָם וּמִקְרֶה הַבְּהֵמָה וּמִקְרֶה אֶחָד לָהֶם כְּמוֹת זֶה כֵּן מוֹת זֶה וְרוּחַ אֶחָד לַכֹּל וּמוֹתַר הָאָדָם מִן הַבְּהֵמָה אָיִן כִּי הַכֹּל הָבֶל:|
Our sages mention that in the most important prayer in Judaism, the Shemah, the difference between the words Echad (one) and Acher (other), is very slight:
Rav Zeira said: “Even parts of the Torah that seem like little slivers ("Kotzin") are actually tremendous mountains ("Tilei Tilim"). They can destroy the entire world if they are not preserved.... [For instance,] in the verse (Devarim 12:4), ‘Hear O Israel, Hashem is our G-d, Hashem is *One* (Alef Chet Dalet),’ if the Dalet of Echad is changed into a Reish by erasing the little sliver that distinguishes between the written form of the two letters, it can cause the destruction of the entire world (because the verse would read, "Hashem is *another*). In the verse (Shemot 34:14): “Do not bow down to a *another* (Alef Chet Reish) G-d ,” if the Reish of Acher is changed into a Dalet by adding a little sliver, it can cause the destruction of the entire world (because the verse would then read, "Do not serve the *one* G-d"). (Vayikra Rabba, 19:2; "Parsha Page," Rav Kornfeld)
The difference between the Dalet and the Resh is simply a sliver, like the Hebrew letter Yud. The Yud represents spirituality. There is a very fine line between what is holy and unholy. Between truth and falsehood. This is related to the month of Adar:
Rabbi [Sholom] Gold pointed out that we celebrate Haman’s downfall during the month of Adar (Alef, Dalet, Reish). At this time, we work on strengthening our perception of Hashem Echad and not bowing down to an El Acher. The mission of Adar is to learn to differentiate between the Dalet and the Reish, and through this, to reveal the "Alef," (which, having a numerical value of one, represents the Creator) whose Oneness will finally be revealed to all when Amalek is completely destroyed. ("Parsha Page," Rav Kornfeld)
The letter Alef itself also has a very special humble/spiritual quality, shared in part by the Yud and the Ayin. This humility is also an essential aspect of the Sefirot of Netzach and Hod. The Alef is the first letter of the first word of the first of the Ten Commandments, Anochi Hashem Elokecha, "I am the Lord your G-d." This Alef is said to contain the entire Torah. Yet what is the sound of this letter? It is silent, humble. It serves simply as a vessel for the vowel. That is the true goal of spiritual service: to be a vessel. That is also the goal of the entire book of Vayikra.