Why should you run frictionless cases? For the same reason it's a bad idea to drive with a hot cup of coffee sitting on the dashboard over the driving wheel.

Sure, in controlled conditions, friction will keep that cup in place.

Without knowing the exact wording, it's difficult to say what they mean about gaps. If it says "non-linear effects like friction," there's wiggle room to say "gaps are non-linear effects, but they aren't friction-like non-linear effects." Thus, I would expect that gaps could be treated differently from friction.