Think of this more like AI War. You start a game, and then you play the game. There are some meta aspects between games in this one, unlike in AI War (achievements aside in AI War), which include things like the missions and the ranks for your profile. But the missions are like Tiny Wings or 10000000 or JetPack Joyride, not like Galactic Civilizations. The model here is actually like Civilization IV or Age of Empires III or similar if you're not playing their campaigns (which I never do). Basically like choosing to play a skirmish in an RTS.
In terms of customizing the board before you start, there are very few options, by design. However, when you first start playing there is a 5-turn "round 0." During this round, resource costs for all buildings and units are completely waived, and no units you place do anything. Time just stands still, and the board does not grow at all without your direct intervention, either (no random lands appearing at the end of each turn, unlike normal).
This round 0 phase is pretty important as it lets you basically configure things to your liking for the start, and skips a boring slow start. But since you have very limited numbers of things you can do there, what choices you make in round 0 will affect the rest of the game. After 5 turns, then it's time for round 1 and everything comes to life and you're off to the races.
In terms of choosing what kind of map you start with, it's just a matter of selecting them from a dropdown. The map types are not randomized at all when you first start them; aka it's always the exact same setup. However, that's just the germ of the map. The real map is created as you play, by both you and the RNG. And so every map is really different not because of options you chose BEFORE you started, but because of what you chose during gameplay (and what the RNG tossed at you).
You can also select what factions you want red and blue to be, how many turns there are per round, and what the sky backdrop will be. Right now those are all the things you can (or really need) to select before starting. However, when the edicts get added, you'll also be choosing two of those like the AI Types in AI War. There will also be a couple of brief multiplayer options. All in all, there's no need for a crazy setup screen like in AI War, because all of the configuration gets expressed through the start of the game as you start playing. Which is something I really love, personally.
There are also no difficulty levels: they simply are not needed. You're your own worst enemy, really. As you strive for missions and top scores, you're pushing yourself closer to the brink of failure. It's kind of a "bring me the whipping switch, boy" sort of system, heh. The edicts will be grouped into difficulty categories, though, so those definitely would qualify as difficulty settings once they are in.