I see your point. However, in my experience, the "same file in multiple locations for valid purposes" thing happened to me many times, but only and always in specific, special directories (for example those where I compiled software). I handle those directories in other ways, including revision control systems.
The scripts I explain here, instead, are specifically designed only for all those times and folders (e.g. archives of my articles) in which duplicates are completely useless, and the sooner they disappear the better; and I only use them in such folders. So I agree with you, it's just that in my own experience the "duplicates that have a purposes" and the "duplicates that have no purpose" never end up in the same folders.
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