Looking around and finally finding the design doc for the game, I do not see the general idea of what Arks and Flagships are supposed to look like.
So far I am imagining the Arks to be something along the lines of the mothership from Homeworld, but I also had thoughts that there would be a visible bio-dome.
(http://mygaminglives.com/wp-content/uploads/2016/03/homeworld-spaceships_00358946.jpg)
Flagships, I am currently imagining look like battleships with visible hangers and sockets for engineer drones (like the scanner drones in Subnautica that sit in a socket in the scanner room), but lacking the space to house sleeping survivors or a bio-dome which explains why they are much smaller.
(https://lh3.googleusercontent.com/vwD1gk2JpP92b4OiaRi8ano1abFQK5m9xv3TbOWeQSGmifnHqyH3WMkJT81AUHhU_sE=h900)
What do other people think they are supposed to look like?