Personally, I think that the proposed idea is too much work and would either irritate players or add more complication to race creation.
However, 2 alternatives come to mind:
1: ethics-based additional greebling as suggested above. Just have textures/pieces specific to each ship type-ethic combination that can be added/removed from ship hulls randomly on ship design, this will also help otherwise-identical ship classes appear distinct. So, for instance, authoritarian ships may have your flag appearing on the side, or militarists may have additional armour plates.
2: non-phenotype based ship sets. I think a reasonable number of players would pay for 8 new ethics-based ship sets. If releasing that much in bulk is too much then having each one released separately as an ethic aesthetic pack, including new race portraits and clothing for each phenotype (functionally identical to plantoids) would also work, though I'd hate to see how the community would react to the release order.