I agree. However, bringing bzip2 compression to .kra is a quick-win by comparison. Krita already have quazip into its workflow so changing that would require WAY more work than just changing a version number for a dependency.
For nowadays needs, ideally, .kra would be compressed with zstd only and its versatility in settings would determine if high compression is done at cost of time or if quick saves are done at cost of storage space. Unfortunately, quazip is already mixed into Krita in some shape or form. It would require changing libraries which would have a different API which might take months if ever approved or picked up by a dev.
Bzip2 only makes sense for .kra because it’s a quick-win development. Ideally, Krita would use a library such as minizip-ng which supports pretty much all algorithms of .zip and has been having a much more active development than quazip.