I had some fun trying to answer your question, so I'll post my answer here. I'm not a specialist, just a pedestrian, so if you want to thrust in someone, thrust in @CosmasZachos
Let $(\hat q,\hat p)$ and $(\hat Q,\hat P)$ the pairs of conjugated variables related by the unitary transformation $U$. We have
$$
\hat Q = U\hat qU^\dagger
$$
and
$$
P= U\hat pU^\dagger
$$
If $\hat H = \hat H(\hat q,\hat p)$ is the Hamiltonian operator, we have(this can be verified through Taylor expansion of $\hat H $and unitarity property of $U$):
$$
U\hat H(\hat q,\hat p)U^\dagger = \hat H(\hat Q,\hat P)
$$
Now let $U=e^{-iF/\hbar}$ for some Hermitian operator $F$. The expression of $K$ turns out to be
$$
\hat K = \hat H(\hat Q,\hat P) + {\partial F\over \partial t}
$$
Now we need to find the Classical counterpart for this transformed Hamiltonian. I thought about two possibilities: Path integral formulation and the Principle of Correspondence. The first is a little bit tricky and, to be honest, I think we should not expect it will work everytime. But I'll let it here, because it was my best try to connect the generating function with the function $F$.
Path integral approach
We can use this relation to define the time Evolution operator. We have
$$
U(t)= e^{-i\hat K t/\hbar} = e^{-i(\hat H + \partial F/\partial t)/\hbar}
$$
Now we can use the basis $|Q\rangle$ for a representation of the above operator and the idea is to build the path integral representation with trajectories in the $Q$ space, yo get the expression for the action related to this sustem. Since the classical action and the quantum action are the same, we can use it to find the classical action. I'll not work all the calculations explicitly, but since ${\partial F\over \partial t}$ could be thought as a function of $(Q,P)$, we can work with it the same way we deal with external potentials when building the path integral.
The kernel is
$$
K(Q,t;Q_0,0) = \langle Q|U(t)| Q_0\rangle
$$
and in the path integral formalism it could be written as
$$
K(Q,t;Q_0,0) = \int \mathcal D Q \,\, e^{iS[Q]/\hbar}
$$
where
$$
S[Q] = \int \left(P\dot Q - H(Q,\dot Q) - {\partial F\over \partial t}\right ) dt
$$
Now I think we need to impose the Hamilton condition for generating functions to connect the above expression with the Hamiltonian $H(q,p)$ that is related to $\hat H(\hat q,\hat p)$ through the Principle of Correspondence. It means we should find a function $G$ such that
$$
P\dot Q - H(Q,P) - {\partial F\over \partial t} = p\dot q - H(q,p) + {dG\over dt}
$$
Now, some considerations:
- There is no reason to think that $F$ could be the generating function since, in the way I worked, it will be given as a function of $(Q,P)$, and a generating function should be a function of old and new variables.
- It seems, by this way, that the function $F$ could be discarded from the expression of the classical action. I'm not sure if it makes sense, but if so, we could discard this term in the last equation above.
Principle of Correspondence approach
We just say that the classical transformed Hamiltonian is
$$
K(Q,P) = H(Q,P) + {\partial F\over \partial t}
$$
and the Hamiltonian condition follows as before. If the unitary evolution does not depend explictly on time, we have
$$
K(Q,P) = H(Q,P)
$$
and the Hamiltonian condition reads
$$
P\dot Q - K(Q,P) = p\dot q - H(q,p) + {dG\over dt}
$$
Some sanity check. For $F=0$, the unitary transformation is the identity and $P=p$, $Q=q$ and we can take $G=0$.
If the unitary transformation is a translation, $\hat F = \alpha \hat p$, so $P=p$ and $Q = q+\alpha$, so
$$
p\dot q - K(q+\alpha,p) = p \dot q - H(q,p) + {dG\over dt}
$$
It's enought to take $G = \alpha p$.