Thank you for the details. It is good for me to know that overlap is not a concern in your use case. I also have a better idea of why the billboards that you are using exists in two entity collections. I do not think that there is a simple way to use Cesium while relying on three.js for more primitive rendering. However, this community forum discussion touches upon some of the rendering differences between CesiumJS and three.js:
Let me know if you have any other questions or concerns!
-Sam