MajinBlayze
It's not quite that simple.
Each package can choose one from a handful of runtimes to use, each of which include common dependencies (like gnome or qt libraries), and if multiple flatpaks use the same runtime, that runtime is only downloaded once.
It is less space efficient than your typical package manager, but brings other benefits like sandboxing.
I'm not sure what the chances actually are, but that much rewriting and shuffling data, if it doesn't immediately result in data loss it is going to put a lot of wear on your drives. If your largest drive is 8 TB, I'd look for another 8+ TB drive so that you can copy the data and then reformat. Even a slow external drive is likely to be faster than what you're doing.
There's plenty of rational reason to hate this video
A VPN is definitely an example of software you should use rpm-ostree to install.
To add some detail, anything you install in a distrobox (or other sandbox/container) can't add kernel modules, which I think is the error you're getting.