Ultimate Admiral Dreadnoughts
I think for a good reference concerning this game's customization, games such as Naval Ops Warship Gunner and Naval Ops Commander should be looked at, at least for comparing and possibly improving/implementing the design phase.
Considering there isn't really any dedicated videos on this game and other in the series this is the best i can provide - https://www.youtube.com/watch?v=uN9JZB7hj0I&list=PLH0DrkuqnKuPXnBcESjfbglWhqAFUSWDN
Now designing like this is possible with the 3D aspect currently in the game, the limitations so far i have came across during gameplay were the restrictions to where you could place certain guns and structures on board you're design ship. The reference i'm providing has no such restrictions unless its ridiculous as seen above (it doesn't fit). If the game is trying to improve and make it more fun i think this kind of design process would really increase creativity with designs. Although you could restrict this somewhat for a more realistic designer if that is what this game is striving toward instead.
Overall i would highly recommend this game as a reference at least, the link i provided also contains a playlist if you feel like skimming through it to check the design process.
Finally the premise of the game i feel is very good, and considering its in alpha stages i really hope this can help in streamlining the design.