I agree with you that if the story is presented from the view point that the infrastructure for all activity already exists in space, then the gravitational fields and atmospheres of planets can be ignored.
If the story starts from such a advanced position, then faster than light travel would be of importance and that is where the "history lesson" to new space cadets comes in.

As I wrote before:

"Perhaps in the story, these solutions can be explained from the perspective of history, maybe a lesson to new space cadets, something like: The Chinese invented the rocket, the Germans improved them, the Russians and Americans used them to travel in space and then in the year 2009 the Zoners figured out what gravity is and how to control it.
And that is how we arrived to the point where we are able to travel easily in interplanetary space.
Our knowledge of gravity and space improved greatly, thanks to the Zoners, we had the framework to figure out that faster than light travel is not impossible, and such knowledge gave us the ability to explore other galaxies."

I agree with you that space is only a "near perfect vacuum" after all there are the protons that are expelled by various stars and the atoms and molecules that escape from the planets and we should not forget the photons that are everywhere, sure their density is not very great but if we travel at the speed of light or faster then all that stuff must be removed from the direction of travel.
In other words, we cannot go faster than light if light is in the way of our travel.