You can create multiple formats and expect your users to understand the differences and select the correct one, but the 99% use case is non-technical users--so

You can create multiple formats and expect your users to understand the differences and select the correct one, but the 99% use case is non-technical users--so 99% of us are going to choose the default option. A bit of redundancy (a short signature and copy of file metadata) is a clear win here, at least for popular formats like Zip. In order for a format to BE the default option for non-technical users, it has to be reasonably good for most use cases, rather than optimized for one specific use case. If you are writing a package manager or backup program you might make a different choice, but how often do you find yourself writing a package manager?