I answered this question in my PhD thesis, supervised by the OP:
https://arxiv.org/abs/2206.11244
In the simplest case, the big crystalline topos over $\operatorname{Spec} \mathbb{Z}$
classifies the geometric theory of a local ring $A$
together with a nil ideal $I \subseteq A$
and a PD structure (divided powers structure) on $I$.
In the general affine case (Theorem 5.7.4), we have a pair of base schemes $\operatorname{Spec} R / \operatorname{Spec} K$, where $K$ is a ring equipped with a PD ideal $I_K \subseteq K$ and $R$ is a $K/I_K$ algebra. Then the local ring $A$ in the theory is a $K$ algebra, more precisely, it is equipped with a homomorphism of PD rings $K \to A$, and the quotient ring $A/I$ is equipped with a compatible $R$ algebra structure.
The thesis also explains how to obtain a classified theory in the case of non-affine base schemes (Theorem 3.7.6 for the Zariski topos, Theorem 5.8.3 for the crystalline topos), by "gluing" together geometric theories according to how the base scheme is glued together from affine schemes.
In all these cases, appropriate finiteness conditions have to be imposed on the objects of the site defining the topos for the classification result to hold. For the big Zariski topos, the site contains finitely presented algebras over the base ring, or schemes locally of finite presentation over the base scheme. For the crystalline topos, we need a notion of finite PD presentation.