Do your footprints not have 3d models? Or does the step export not include them? Because i would really not add something to the design just to have a reference point for 3d modeling. This would be best done in the 3d models assigned to the footprints.
Oh and are you aware of the stepup extension for freecad? Kicad StepUp: a Seamless ECAD/MCAD PCB Data Integration