usually when i start i do a sort of tower with 10 houses on each side and my tools and chests on the bottom. Its quick and easy for the beginning, but my above picture is me going for something different. Still ended up with a few copy-paste like rooms, but its far nicer looking than a wooden tower.
Plus i don't use doors to get in. I use a player activated Actuators on glass so that enemies don't get in but i can run out seamlessly. That teleporter goes to my old base, which is almost fully cleared out.