If there's no physical connection, what are you expecting to see connected to the node? Is it parasitic capacitances from other layers to this substrate? If so, probably what you want is the Ref Node on the Extraction tab in the Assura RCX form. Any decoupled capacitors (or capacitances to "ground") will be connected to this node.
It's not that clear to me quite what you're trying to do.
Otherwise if it's a physical shape in the layout, do you need to just label it? (in which case that sounds like a "physical connection" to me, so I'm not sure that's what you're after).