Not completely impossible, It will cut away, though it is a soft cut and if you make the negative MB with a different material, it will transfer that material like other metaballs, (gradient transition)

Be cautious, metaballs take a long time to render, and their properties make the scene very KB heavy, and likely to crash or lock on you. Save, save,save, your file as you work on it.

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Ockham's razor- It's that simple