Yes, sandboxing impedes those things. But I assume you're not advocating against sandboxing in general, right?
Starting with a sandbox and poking holes/whitelisting as-needed is a good way to go. Whitelisting access on a per-application basis is a pragmatic way to do this, and Flatpak with Wayland gives a way to actually implement this. It's imperfect, but it's a good start.
Preventing keylogging is a good, concrete example here. There's no reason some random application should be able to see me type out the master password in my password manager.
Likewise, there is no reason that some other application should be able to read ~/.bash_history or ~/.ssh/. The browser should limit itself to ~/Downloads. Etc.
> Meanwhile the advantages of sandboxing are pretty much moot in an open source distro where individual applications are open and not developed by user hostile actors.
Defense in depth. Belt and suspenders. I do trust the software I run to some degree, and take great care in choosing the software. But it's not perfect. Likewise, I take care to use sandboxing features whenever I can, acknowledging that they sometimes must have holes poked in them. But the Swiss cheese model is generally a good lens: https://en.wikipedia.org/wiki/Swiss_cheese_model
If we weren't concerned with belt and suspenders and could rely on applications being developed by non-hostile actors, then we could all run as root all the time! But we don't do that--we try to operate according to least-privilege and isolate separate tasks as much as is practical. Accordingly, technologies which allow improved isolation with zero or minimal impact to functionality are strictly a good thing, and should be embraced as such.