First of all, according to the devs, there are only two forms of propulsion in the game right now, hover engines, which will let you get up to 1km off the ground, and your normal thrusters that will take you into orbit. There are no wheels or other "ground based" vehicles. You will be flying, hovering or walking. I see no reason why you couldn't build a large mining vessel like described above to work in atmosphere. And from the sound of things, you're going to need something like that early in game, because you're not going to log on, mine for an hour, and be in space. You're going to spend some time on the ground before you rocket off into space.
And as far as fuel costs.... if you're in a mining vessel, and fuel is mined like Uranium or Ice in Space Engineers.... doesn't it make sense that you would be mining fuel too? Wouldn't you then be fueling yourself as you go? Bam. Fuel problem solved.
This does bring up one question in my mind... if everyone starts off in the same arcship and has to mine.... at what point is the arcship the only thing left on the planet? Does the server reset all the mined areas of the planet, like EvE regenerates asteroid belts? Because you know there is a carebear organization out there somewhere who's only goal in life will be to mine an entire planet. And if so, how does the game differentiate between a massive hole dug solely for mining purposes, and a hole I dug to hide my base in, but I ran out of time to place a structure in there before the server reset all the mined areas.... I'm glad I just play and comment on the games. lol.