The hidden train stops are actually connected (at least in the latest version). The GUI of the train stops just doesn't show it.
If you unzip the mod, open data.lua and add these 3 lines:
draw_circuit_wires = false,
circuit_wire_max_distance = 9,
circuit_connector = circuit_connector_definitions["train-stop"],
to the invisible-train-stop definition then the circuit connection box will show when you select one of the extra Stops of the train stop.