I don't know how feasible this is, but it would be nice to have this ability, since there's a possibility the overlay files might get messed up and that would be migrated to the next deployments, like in this bug that you've found.
One way I think this might be possible is to simply backup the overlay files right after the user account creation and store them in a certain location. Then, the restore could be invoked via a new arkdep command.