Fluid volume extraction also does boolean operations in the background. You are right for geometries having many bodies, subtraction operation works many times.
Are these duplicate faces in the same body? If it is a solid body then how it can have duplicate faces? Can you please check duplicate faces for a single body and insert image here? The image you have posted does not give any information about how many bodies are visible. Please insert more images with more explanation.
Regards,
Keyur
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