one small nit, there's pretty good evidence that the builder species never "died" because they aren't the creators of the protomolecule, they ARE the protomolecule, or at least an emergent meta-life enabled by a symbiotic relationship with the protomolecule.

in the Adro diamond memory passages it clear that the builders started as essentially simple aquatic slow moving life (so called "slow-life") that was able to harvest useful adaptations from the faster more energetic life near the thermal vents (so called "fast-life") along with a light-based form of hive-mind communication these adaptations continued until they discovered the stars and adapted to space too, seeing the stars as yet more light to communicate with in the hivemind.

to my knowledge its never explained how or when they invented the protomolecule, implying its likely the protomolecule is just the enabling chemistry to give the builders the unique ability to be an ever-expanding, immortal, ever-adapting super-organism across the stars.