For example, the story of Avraham Avinu and Sara Imeinu isn't only about the actions and interactions of our first Jews. It also represents the actions and interactions of the Sefirot in a completely different dimension. In addition, there are many more layers of meaning to every word of their story inscribed in the Torah.
In other words, the Torah is not only true, but it's truer in more profound ways than we could ever imagine.
For example, the Kav Hayashar Chapter 42. He refers to a well-known section of the Chumash that seems to "only" discuss an aspect of Jewish Law. Yet the Kav Hayashar gleans from the Zohar an underlying lesson for which the halachic description is pure metaphor:
It is written-- “And when the daughter of a Kohein shall be widowed or divorced, having no offspring, and she returns to her father’s house as in her youth…” (Vayikra 22:13) [and in the previous verse it is written,] “…she shall not eat of an offering of the holy things.”
According to the Zohar (2:95b; 3:7a) this is an allusion to the soul.
The soul was created to enter the body in order that it should be rectified and adorned with good deeds.
But when a person transgresses, he blemishes his soul, causing it to cry out to Hashem, saying, “Hashem has delivered me into the hands of one against whom I cannot stand” (Eichah 1:14).
When the Holy One Blessed is He hears this cry, He says to the soul, “My precious daughter, you were raised in illumination and honor beneath the Throne of Glory and were called, ‘precious daughter.’
"Then I lowered you into a human body, intending to elevate you to the highest levels through that human being’s good deeds. But now that he has sinned you have been degraded, plummeting from a lofty rooftop to the deep pit of the human body.”
At this point the soul becomes known as a “divorcee” because it is banished from its place against its will (“divorced” and “banished” are expressed by the same word in Hebrew).
But Hashem hears its cry and takes the soul from the body and purifies it though chastisements, after which it is able to relish the delights of its Heavenly Father.
So yes, this scenario as written in the Torah provides us with guiding laws and insights.
But there is also the whole other hidden meaning described above, which seems unrelated to the straightfoward meaning, yet has everything to do with it.
And this still isn't even the whole meaning behind these verses. There's much more, but this is enough to make the point.
The above is just one of many reasons why rationalist arguments regarding the Torah fall short. The Torah and all it encompasses is far, far more than the 3 dimensions we perceive.