I honestly prefer current distinctive appearance. Ruining their tree-like image just to make them look closer to domain technology will be great mistake. I don't think it is immersive to make Tri-Tachyon the only faction that has own shipbuilding school with distinctive style. It is normal and expectable for factions, that existed regardless of Domain to avoid using domain tech and copping Domain style.
Also looking around at the real world you may see that even on a single planet that has become to small for someone to hide effectively most efforts to limit and control technology eventually fail. It is quite clear that at the imaginary Domain scale attempts to limit access to nanotechnology and control it's usability and development by enforcing copyrights, patents, DRM and so on will fail even more miserably. Actually if there is something that is really not immersive in SS it is the assumption that such powerful state system formation existed without enforcing ban on R&D of high-end nano, bio and field manipulation technology, destroying systematically anyone who attempts to violate it. Actually they would have preferred to simply bury such dangerous things. The fact that they still used nanotech is most likely evidence that control was lost even before the Domain was able to react to it's development and when they become aware of it the tech was already available to a number of presumable enemies.
This makes safe to assume that in Domain controlled territories nanoforges and their control chips have become available to the general public only after collapse (mostly due to uncontrollable scavenging), but remaining/new states still do their best to prevent any uncontrolled "creativity" in their use (including taming the population to perceive tempering with blueprints or chipless nanoforges as abomination on pair with unbound AI). Territories that where out of Domain reach however eventually gained their own nanotech infrastructure, developed own blueprints and enforced their own nano tech control policy long before the collapse.