The upshot is that the Rationalist and Mystical approaches are not mutually exclusive. Mitzvah observance can improve a person’s character and also have metaphysical resonance.
I don't dispute this in theory; there's no reason why a mitzvah can't have more than one function and benefit. But I do dispute it with regard to the specific case of the Zohar's explanation of shiluach hakein. R. Student argues as follows:
While I find his study useful, I am unconvinced by R. Slifkin’s dichotomy. These two approaches are not mutually exclusive. Yes, one sees the sending away of the mother as an act of compassion and the other as an act of cruelty, but they can both be true. It is, from a bird’s perspective, tragic that her eggs are taken and she is sent away, but it is still a more merciful and compassionate way of taking the eggs.
There are two points to discuss here:
1. Would/ did the Rishonim/ Acharonim have accepted this reconciliation?
2. Can we accept this reconciliation?
Let's begin with the first question. Obviously Rambam and others who rejected kabbalah would not accept the Zohar's mystical explanation of the mitzvah (and I am not sure that Rambam would accept R. Chaim's view that a ta'am for a mitzvah is just a taste, not the reason). Furthermore, R. Student is forced to adopt the mystical position that it is praiseworthy to send away the bird even if one does not want the eggs; but Rambam explicitly writes that the Torah's ideal is that one will leave the nest alone entirely.
R. Student points to Ramban who says that there are mystical reasons for shiluach hakein as well as compassion. But Ramban does not give the specific mystical reason of the Zohar, so this is not relevant. As mentioned earlier, I am not pointing to an inherent conflict between rationalist and mystical explanations of mitzvos across the board, but rather to the specific mystical explanation given by the Zohar.
Clearly some later authorities, such as R. Baruch Epstein, saw the mystical approach as irreconcilable with the rationalist approach: "It is clear that the Torah is only granting an allowance with this, but with someone who does not all want to involve himself, it is certain that he is permitted to simply pass it by. In fact, he is making things even better for the mother and young by leaving them together."
And so on. I think that an analysis of the Rishonim and Acharonim will show that, at least for the most part, they were taking either the rationalist or mystical approach, and rejecting the other.
But is it possible to create a reconciliation, along the lines that R. Student suggests - "It is, from a bird’s perspective, tragic that her eggs are taken and she is sent away, but it is still a more merciful and compassionate way of taking the eggs"?
As appealing as this may be, I'm afraid that it's trying to square a circle. From the mystical perspective that the Zohar's explanation is correct, and the point of the mitzvah is to arouse Divine compassion upon the Jewish People by causing distress to the mother bird, doesn't this mean that there is a correlation between the amount of distress caused and the amount of compassion brought for the nation - and if so, why would one minimize the amount of distress by not having the bird witness you taking her young? Isn't it better for the nation that she is more distressed? And why not be cruel to non-kosher birds and other creatures, in order to have their angels complain and further bring about compassion upon the Jewish People? Wouldn't that be in the spirit of the mitzvah - or at least a good way to improve our national fate?
Conversely, from the rationalist perspective, there's simply no reason to postulate the explanation (and subsequent ramifications) of the Zohar - which is why the Rishonim didn't do so - besides the issue of whether it has any credibility as an authoritative source (as per Chasam Sofer). Furthermore, it goes against the entire worldview of the rationalist approach, as explained in my essay. One earns Divine compassion by being compassionate, not by mechanistic manipulations of angels and God which involve committing precisely the sort of acts that are ordinarily antithetical to Torah values.
We like to think of Judaism as a homogeneous, unified entity. It would certainly make our lives simpler if it were that way. Unfortunately, it's just not the case. But maybe one can take a more positive perspective on this, and conclude that Judaism has developed into a way of life that can offer meaning to very different types of people. (Although in the specific case of shiluach hakein, I can't say that I'm comfortable with the meaning that it offers to mystics!)