I see what your are saying, but in other use cases the presentation state needs to be considered as part of the document. This is one of the reasons zip/jar containers work somewhat well. You can audit different chunks of data separately and cryptographically sign them. sqlite actually has an archive format[1] that is interesting to think about and I have pondered using it for some applications (store the files and also store tables of metadata/analysis)

[1] https://sqlite.org/sqlar.html