> Also, the compressed archive could have been structurally baked in a specific way that's meaningful to the customer.

EPUB is an example of this. They're mostly bog-standard ZIP archives, but in order for the file to be valid, the "first" file in the archive, linearly speaking, must be named "mimetype" and stored with no compression (each file in a ZIP archive can have a different compression level). If you just unzip an EPUB and then just dumbly zip it back up again, your end file will not be a valid EPUB.