I don't know of a notion of "logical functor" between predicative topoi that specializes automatically to the standard notion if they happen to be elementary topoi. But I do know a definition of "logical functor with a left adjoint" that has this property, and this is sufficient for the purpose of defining atomic geometric morphisms, since a logical functor between elementary topoi has a left adjoint if and only if it has a right adjoint, so it is equivalent to say that $f^* \dashv f_*$ is atomic if $f^*$ is a "logical functor with a left adjoint".
The definition is: if $F:C\to D$ has a left adjoint $L:D\to C$, then $F$ is logical if and only if $L$ (not $F$!) induces isomorphisms of subobject lattices $\mathrm{Sub}_D(X) \cong \mathrm{Sub}_C(LX)$. The fact that this is equivalent to logicality of $F$ follows from the Yoneda lemma: we have
$$\mathrm{Sub}_D(X) \cong D(X,\Omega_D)$$
and
$$\mathrm{Sub}_C(LX) \cong C(LX, \Omega_C) \cong D(X,F\Omega_C)$$
both naturally. Thus, the left-hand sides are naturally isomorphic if and only if the right-hand sides are, and the latter is equivalent to $\Omega_D \cong F\Omega_C$ by the Yoneda lemma.
In this blog post I used this characterization to suggest a notion of "$\infty$-atomic geometric morphism" between $(\infty,1)$-topoi.