You are correct, Cocos3D is not compatible with recent versions of Cocos2D and SpriteBuilder.
Development is underway to provide compatibility with the future versions of Cocos2D and SpriteBuilder, but it will likely not arrive for several months.
In the meantime, your best bet is to use the earlier compatible versions of Cocos2D 3.2.1 (or here).
Since SpriteBuilder is an AppStore app, it's intended to be used only in the most recent version (no pre-built back versions are easily available), and retrieving it from GitHub to build an earlier version is challenging, to say the least. For the time-being, I recommend that you avoid using SpriteBuilder with Cocos3D.