Alpha channels are having a weird effect where they clip through geometry behind them. I am using 3d shapes for the smoke effect. the world is a 3d object
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Yes, transparency/alpha in 3D, in general, is always a challenge. The better results for simple renderers like C3 are to render in order as much as possible.
Check that the render order is the distance from the camera and all layers are 3D.
If your 'world' is one big GLB/GLTF model, it will be hard to sort properly (near and far meshes will all be part of one model.)
An alternate option is the 'screendoor transparency' in the 3D effect, which has a particular 'look' but will make the rendering support out-of-order rendering better.
DAN