I think it was intentional since it's been like this since I bought the game and it helps you colonize faster; it gets the game moving.
Yup, it's definitely intentional. It can also be changed per map. In beta, the flagship actually started at level 3 also
Annatar, Did i understand you correctly? The Capital Flagship started at level 3? Meaning it jumped 1 and 2? Or meaning you didn't get it until you reached the third level with one of your other caps?
That sounds awesome!!! I would love to find a way to start a map with a cap at different levels, i could build "crews" then and have a ship go from game to game at a sequential leveling up!! Like having a Carrier captained by Jameson Faragut and going through 5 games and twelve levels!! That is the other thing i am working on, trying to get the caps above level 10.
Not that it will ever happen, haha, but its worth digging around in the files trying to figure out if i can do it. 
-Teal