You could have something like this:

    public class SetupXml
    {
        public SetupXml()
        {
            SubSetups = new Collection<SubSetupXml>();
        }

        [XmlIgnore]
        public Collection<SubSetupXml> SubSetups { get; private set; }

        [EditorBrowsable(EditorBrowsableState.Never)]
        [GeneratedCodeAttribute("Whatever", "1.0.0.0")]
        [XmlArray("subSetups")]
        [XmlArrayItem("subSetup")]          
        public SubSetupXml[] SerializationSubSetups
        {
            get
            {
                return SubSetups.ToArray();
            }
            get
            {
                SubSetups = new SubSetups();
                if (value != null)
                {
                    foreach(SubSetupXml ssx in value)
                    {
                        SubSetups.Add(ssx);
                    }
                }
            }
        }
    }

It's not perfect, but the EditorBrowsable attribute will prevent developers using this library (from another assembly) to see it displayed by intellisense/autocompletion tools. And the GeneratedCode attribute will prevent CA warning on it.