Docker and Flatpak use storage in different ways, despite both being implementations on top of Linux namespaces/cgroups.
Docker uses layered images, one on top of another for each step of the build process, to deduplicate in Docker, you try to reuse layers, but it's not perfect and having duplicate files is very very common.
Flatpak uses OStree, which has a content addressable file store, meaning files are stored and linked based on their checksum, so duplicate files only exist once and are linked into their respective locations.
There is work to make Docker use a system similar to Flatpak (see composefs).
Docker uses layered images, one on top of another for each step of the build process, to deduplicate in Docker, you try to reuse layers, but it's not perfect and having duplicate files is very very common.
Flatpak uses OStree, which has a content addressable file store, meaning files are stored and linked based on their checksum, so duplicate files only exist once and are linked into their respective locations.
There is work to make Docker use a system similar to Flatpak (see composefs).