Hi Justin,
I am sorry for not being precise in my last post; when I am referring to can see/not see, I am referring to giving user permission to go into it to view & run job from it.
Currently, with the automation engine (in the Java client); there is no way to "hide" the top level folder object that you do not have permission to. If the user who don't have permission to it, they won't be able to drill down deep to view what object is within those specified folder and so they will just see the top level folder object (even if they don't have access to it).
Its is not as glamorous and clean as you have wanted but currently it is the only way within the Java client, for having multiple department/business unit as such within the same client (beside having each department/group in their own client).
We recently have a few other which have asked for this feature to "hide" top level folder object they don't have access to. It is currently being assess by our Product Management but I would recommend also
submitting an enhancement request with them so they are aware of the volume of this feature request.