Regardless of the original intention, the lower winglet serves almost no aerodynamic purpose, as you acknowledge. It does, however, provide physical protection from a wing strike. So I stand by my statement that its purpose (now) is the latter. If you're not worried about hitting the wingtip then remove the lower winglet as many have done (speaking about the VariEze only).
By the way, assuming that data was available at the time, it seems likely Burt knew that the lower winglet wouldn't contribute much aerodynamically in normal operations.