I have also found that my 20" folders are about 10% slower than my go-fast Swift, and the 16" ones closer to 15% slower.

My take was the smaller wheels, the tyre types, the weight, the flexiness, the hub gear drag. In your setup I would ditch the Marathon Plus and use Kojaks, with a tyre liner in the back for puncture protection. That's what I have on my Brommie. I just this week installed a Schlumpf Speed Drive on it and I think I can feel the drag, but since I am not looking to save every joule on the Brommie, I am not too fussed.