Question

A question that has been bothering me for a long time—
As is well known, the Jewish law follows Rabbi Yehuda that one who stipulates contrary to what is written in the Torah—regarding monetary matters, his condition is valid.
Meaning, in practice almost all the clauses in Choshen Mishpat are dispositive rather than mandatory.
Of course, in any legal system there are mandatory provisions and dispositive provisions that serve only as default rules,
but in our case this is very hard to accept—

1. The scope—there is no legal system that determines that all provisions relating to monetary law are dispositive.
2. Substantively—if the Torah is not an ordinary human law book, but rather its purpose is “the application of the divine abundance upon our nation” (in the Ran’s formulation in his homilies), then I would expect that most, if not all, of its provisions would be absolute, without the possibility of stipulation. What meaning do the Torah’s monetary laws have if they are only in the nature of a recommendation / default rule? If the default rule is nevertheless more “recommended” than the others, why was the possibility given to create a different legal framework? And if it is not more recommended than others, then where is its value?

(I am familiar with the explanations of some of the later authorities (Acharonim), according to which the Torah’s law does in fact apply to the parties, except that each side waives its right, and the like—but that does not resolve the essential difficulty.)