> For example, they don't duplicate exact versions of dependencies on disk.

Doesn't feel like GoboLinux would either, does it?

Flatpak's complexity is also a product of trying to function as a single solution to two different problems. Runtime isolation and packaging/distribution are different things, and there is no compelling reason for them to be conflated together. How you sandbox the execution of your applications should not be dependent on any particular filesystem layout or package format, nor vice versa.

FreeBSD does a good job with this: applications are installed into a standard Unix filesystem with conventional packages and the ports collection. Isolation is then implemented via jails.

The Linux equivalent of using standalone isolation layers, like firejail, on top of standard distro packaging, is far superior to Flatpak.

You are aware that windows has each app on its own folder in program\ files and its completely fine. ext4 supports an insane amount of files, so much so that unless you're doing something really out there, you're never going to reach the limit.