Proto means "first," or "in the earliest form." And yes, you are starting with the seed of a colony that you are just starting to develop. Your foes (and potential allies) are already well established (unlike Civ games), while you are just this puny landing party that is growing into a larger colony to rival the others. Empire is frankly kind of a misnomer here anyway, because the scale of this game is a bit lower. You aren't building many cities like in Civ, but rather are building fewer but way more detailed cities. A "city" in civ would actually be more analogous to a "city hall" here, and then the various tile improvements in civ would be more like buildings here.
You'd have multiple cities here, just as with civ, but each of these is more complex in terms of how many tiles they take up and what is on the tiles. Closer to SimCity. So the feeling of a deeper interaction with each city will be there (I feel), but at the same time it's not as abstract a sweeping sense of massive nations.