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.
This model has Ti so it will be springier than steel, but I have the stiffest suspension block. So I was forced up to Marathon Plus reluctantly via punctures from anything less, the wheels came with Brompton's tire, they claim tougher than the Kojaks, lasted only a few weeks then just metal road debris total instant flat, fortunately a block from my home.