In a forum post titled Free Form Characters the developer Casey McGeever aka "The Consultant" discussed Free Form Characters stating that Ship of Heroes will not include a free form build option.

We had this discussion early on, in the planning for SoH. Several of us also played CO and had this experience. Pyrion channeled my personal thoughts about ship of soloers perfectly, but all of the other pluses and minuses are pretty much as you guys have called them.
We decided against free form characters.

Not much else is known at this time.