As a very general rule - Planets are very large things. They tend not to be at all perturbed by very small things (like singleships).
And, as another general rule, avoid saying, "that can't happen". Sci-fi has a long tradition of playing with concepts, and in every age, folks have said, "that can't happen", and later been proven very wrong.
Maybe on Naboo the "land" is really composed of a coral-like material that is overall less dense than water, so that it floats upon the sea.
And getting a lightsaber to be a given length isn't all that outrageous, if you know anything about wave mechanics. It isn't difficult to come up with a superposition of waves that gives you positive intensity within a small region, and basically zero intensity elsewhere. Not that we know the physics of lightsabers, but we already have concepts in current physics that can "no prize" it.