SSIS Rollback Package

I would design each package as a self-contained unit that can be rerun without any manual preparation or clean-up. Relying on SQL transactions can dramatically slow execution and as you noted does not cover all the non-SQL Tasks.

Your precedent constraint defaults to an AND situation. The preceding task must return success and the expression must be true.

In binary scenarios like this, only one of those two tasks is ever going to happen. By adding the next level of constraint in - both tied to the message box step, the final step is waiting for the "Enable CLR on server" to be successful as well as "CLR Enabled on Server" to be successful and for the value to be equal to 0.

Since only one of those situations will work out, you need to swing the PC to be OR situation

That results in the green dotted lines instead of solid

As an FYI, in your Script task, assuming this runs in an automated fashion (SQL Agent), since you're using a message box, it will fail. There's a System level variable, System::InteractiveMode which is a boolean. It indicates whether you're running in an environment where you can interact with the desktop or not. If that evaluates to false and you attempt any GUI activity, the package will error out.

I find it helpful to add code like the following

public void Main()
{
    // TODO: Add your code here
    bool interactiveMode = (bool) this.Dts.Variables["System::InteractiveMode"].Value;
    bool fireAgain = false;
    string message = "This is some message I likely built out using other SSIS Variable values";

    if (interactiveMode)
    {
        MessageBox.Show(message);
    }

    this.Dts.Events.FireInformation(0, "CLR Check", message, string.Empty, 0, ref fireAgain);

    Dts.TaskResult = (int)ScriptResults.Success;
}

There I have a check against my interactive mode and only attempt to display something if I can. I also go ahead and fire an OnInformation event because that's automatically logged in the 2012+ Project Deployment Model, shows in both the GUI and the Output panel in Visual Studio/SSDT/BIDS and is easily recorded from DTEXEC.exe call by appending I to the reporting parameter i.e. /rep EI