@foxxy
Dependency tree of packages: they must be integrated, only one version of libraries, some software can't be packaged, some combination of packages are not allowed.
All-in-one bundles: not feasible to maintain the libraries updated, huge security risks and more resources used.
OSTree deployments: make different version of every kind of file available to different processes but deduplicate the storage by storing only the diff.
(and Flatpak has a sandbox, permissions system etc...)