The runtime thing that flatpak supports is, ironically, to minimize and deduplicate common dependencies, and to be fair they are only downloaded with the first app that needs it with many apps using the same handful of runtimes. The fetish for shared dependencies within Linux and the pains it causes are a bit frustrating, but that's not new to flatpak.
> What's even more insane is at the command line when you Tab to autocomplete the thing makes network requests and hangs! It's the only CLI app I know what requires the internet to autocomplete!
nit: CLI tools do not implement auto-complete themselves. What you are seeing are auto-complete scripts for your shell that make network connections.
Not sure if flatpak keeps a local repo list. That would be the only way to implement tab-completion of installable items without making network connections.