I've never done it myself but I think what you do is start a solo game from one of the two scenarios and quit. Go into the folder where the solo world save file is stored. Copy it and upload it to your server. You'll need to set you spawn somehow to that correct location and somehow you'll need to get a quest book and the starting items.
You need to play in a scenario world because there are starting items you need, the oxygen collector, saplings, bonemeal, etc. If you generate a world (its been awhile so I don't know if it is even possible to generate a brand new world) it won't have those starting things.
With agrarian skies I've changed a parameter and a map gas been generated, so I think it's possible with galactic science, but I don't know how x)