

What does it mean to “make Linux secure”? What does secure mean to you (genuine question). I see people say they can make Linux secure but from what kinds of attacks. I think madaidan’s blog explains why you can’t as an individual fix an issue with the entire ecosystem, or fix the kernel of its inherent security flaws https://madaidans-insecurities.github.io/linux.html
I think “good security” in my personal opinion means that even if you try to run a malicious app, it either crashes out right or can’t do anything because it doesn’t have the permission to.
One thing that I think is very misunderstood is that messy or extremely large/dense code can be very hard to understand, even if you have the source code. Like systemd, it is several million lines of code and is very tangled together. Is it that much better than a blackbox if no one can audit the whole thing (unless you are a massive team)? I do think it is better to have source code and documentation, but vulnerabilities arise from unintended interactions in the code. The more code there is, the higher the chance of this happening.

On the first laptop the missing folders are likely to do with the fact that the Flatpaks are installed as system Flatpaks, therefore installed under /var/lib/flatpak (iirc). Flatpak is configured to let you install them as system wide Flatpak apps, meaning other users on your computer will also see them. It would normally require authentication to do that, but many distros configure it to be easy by default.
The second laptop is installing them as user Flatpaks, meaning the folders (mostly shared libraries, desktop entries, and apps) are stored in the user’s home folder.