My experience is that the rear suspension both of the Moulton Speed (note that the Moulton AM and older models have a different rear suspension) and Birdy do not cause an efficiency loss.

The main benefit of suspension for speed on rough road comes from the front suspension that makes the bike safer while the rear mainly affect the comfort.

I have also a Brompton, a superlight with titanium fork and rear triangle, on cobbles the front wheel bumps from one cobble to the next and force the rider to reduce its speed.

The problem of the Brompton is the combination of small wheels + rigid fork + narrow high pressure tires.

I am afraid that the same will happen with the very rigid single arm fork of the Helix.

The bigger wheels won't help a lot because the tires are too narrow and too high pressure. Peter should have made the frame to accept 50mm wide tires (which is the most common width of ETRTO 507 tires).

I have a titanium frame with carbon fork road bike with even bigger = ETRTO 622 high end wheels and even with 28mm wide tires, the same happens.

The only clear benefit of bigger wheels is on soft ground, sand for instance, where the smaller wheels are blocked faster. But also in this case, wider tires are needed.