Linux

Discover itself doesn't care about security - it's the underlying package manager(s) that do.

Flatpak is perfectly safe IMO, as are the built-in repositories.

Both Flatpak reviewers and Debian maintaniers do their due diligence when auditing the software they distribute.

When using distros/repos which are less FOSS purist (such as Ubuntu), you could run primarily into privacy issues. When using smaller ones, the risk of a backdoor or voulnerability is a bit larger, as less eyes are on the code.

That being said, the only way to be immune to untargeted cyberattacks is to be offline, which isn't reasonable in this day and age. As long as you stick to your distro's repo and Flatpak you should be perfectly fine, save for the "normal" voulnerability or two that unfortunately slip through every now and then. You could think of this as a kind of digital "herd immunity".

As long as you don't add repos willy-nilly but think about who you trust, you should be fine.

So yeah - you can assume Flatpaks and the Debian repos are safe. They have good security policies about adding stuff in and do do their due dilligence. Though, this might change in the future, alrhough it doesn't seem likely. But for now - you'll be fine.

The only real risk is if a backdoor like the recent one in xz-utils does slip through the cracks, but then you'll be one of millions of affected machines which, while not mitigating the vulnerabilities per se will at least mean the problem will get fixed sooner once it does get found.