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Assets in prefabs are exported into the directory the prefab is in when `Export group assets by` is set to container path.
This is problematic when there is a container with a lot of prefabs with similar (or the same) file names.
I'm sorry I didn't understand your question, can you describe it in detail.
Lets say we have a container with a bunch of prefabs, all of the prefabs having a model named model and a texture named texture. If we export via container path, all of these models and textures will be placed into the same folder and given random suffixes. I would expect having a folder for every prefab.