The 3.9GB is not just libreoffice, that number also includes runtimes. At most you would only install maybe around half of your host systems’s packages in runtimes for all the apps you use. There shouldn’t be any more usage than that. And even less if you stick to apps that fit your DE. Like if I just stuck to apps that used the gnome runtimes, I would have a pretty minimal installation.

Unfortunately, the dependency problem is really hard to solve, and at least they deduplicate what they can. Everything else works perfectly as well besides some minor issues with the sandbox connecting to the host system in certain edge cases.

Also please don’t link flatkill, it’s woefully outdated and every point on there has been addressed for years; it should be taken down.