My Swedish eggs are the same size as the Appleyard eggs, even though the Swedish ducks are half the size. Both breeds lay enormous eggs. It seems to me that runners lay huge eggs also,
Eggs can vary in size from day to day. My breeds are housed separately, so I know who laid the egg, but when I box the eggs up, sizes vary enough to be visible without weighing them. Using size for something as critical as raising purebred ducks would be risky.
My ducks lay early in the morning and ducks can be trained to separate themselves into different housing at night. If you simply separate the Runner and don't let her out until after you've collected eggs, that should resolve the issue. Have the 2 pens side by side, with wire, so they can all see each other and everybody will be fine with that arrangement.