Revenge against God for the crime of Being.
Runabouts are just big shuttles, and they land them on planets all the time. Sometimes without even crashing or being stranded! One G and one atmosphere is entirely normal operating conditions for them. (Obviously they can't go to warp while in atmospheric flight but nothing can. )Anyhow, science wise, it was probably explained at the start but that tiny Rubicon ship was made to fly in outer space , right? But it was just floating inside the Defiant, which has artificial gravity. How could the ship operate then? Unless it was built to expose actual planets with atmosphere or whatever, then it would just be grounded with no flight thrust or whatever.
No, the science hole you don't want to fall down is questioning whether materials compressed by the anomaly have any properties changed other than their size. The ship is luckily a sealed environment, so you don't have to worry about whether the Szalinski kids can breathe normal oxygen molecules with their spatially compressed hemoglobin. But light is light and nanometers are nanometers, so they should be seeing in ultraviolet when they look out the windows. And if the Rubicon retains its full mass, then whatever thrust or repulsion is allowing it to fly should be doing a number on the Defiant's deck plating. I expect the mass to be the same because the compressed matter has to more or less retain the properties of its full size self, and shouldn't actually behave like a scale model of itself made with a tiny fraction of the material. For one, you couldn't make normal functioning cells and computers and things at that size out of normal atoms, and anyway the Scalinskis would be transparent, and also dead of radiation poisoning from the warp core since its shielding would be too thin to stop anything.
If you're wondering how he eats and breathes, and other science facts....