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In NTFS any way clusters are already 4k for most modern computers (with 200+ GByte drives) so the smallest allocation is already 4k. Having a 4k sector without any shenanigans just makes it impossible to go below a 4k cluster. Alignment would certainly be an issue but with alignment on 4k boundaries most people would not notice any increase in slack space as since the file system already typically allocates a minimum of 4k. You can do less (on 512K sectors) but then more memory is required to cache disk info.
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