I don't know much about the different compression formats but they all seem to store some amount of file metadata (timestamps, permissions etc). Maybe some form

I don't know much about the different compression formats but they all seem to store some amount of file metadata (timestamps, permissions etc). Maybe some formats store them as part of the compressed data which would result in data loss if files were deduplicated. There are ways around that of course but maybe the .rar format doesn't lend itself well to that.