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That is due to the difference between using the C3 renderer (the runtime C3 engine for rendering Quad3D) and using a separate dedicated 3d engine (three.js or other), there are pros and cons with both. Obvious pros for separate engine are performance and features. Pros for using C3 engine is better integration with C3 other behaviors, effects and rendering order for integration with other C3 objects, like sprites, etc. (sometimes the custom engines will render on top of or behind the normal C3 render canvas).

I made the choice to try to integrate with the C3 engine as much as possible, to make it like a regular C3 addon.

I think the other options are really interesting and definitely worth exploring as a dev. If you only want to use 3D from the custom engine and it has also the ACEs you need it could be a great way to go.