At present we have set of BindingFlags to discover methods for UDFs, they explicitly ignores protected methods. But the attribute based discovery should be done regardless of protection level.
The protection level restricts user's ability to use the method inside of the EF Query but if in some way user can use it then we should translate it.
One way to use the method is to pass in IQueryable to public method in DbContext which would apply logics from protected/private methods by calling them and return it. (or there is always reflection)