The only reason why they do that is because of FlatPak being sandboxed. You’ll have 10+ copies of the same library across multiple applications, which is stupid in comparison to a shared library setup which takes up much less space.
As much as I love FlatPak and Snap in concept and understand how much dep hell it can prevent, I would rather just different version packages for different software. If something needs to be that specific to require its own libs, I wouldn’t mind it. And reallly, that is this topic’s target — the user who installs conventional packages, and maybe the occasional sandboxed software.
Not to say you’re wrong for what you’re doing, testing is great! And not everybody is conventional, nor should follow my advice. @Persephone should evaluate what software on the system is necessary and one’s own use habits before committing to the above advice. But I believe I provided sane defaults for most people trying any Linux system out.
Per my understanding, this configuration makes backing up more tenable for the average user than what OEMs provide for Windows by default because less thinking and configuration is involved. It can better integrate into a typical user lifestyle so when stuff goes wrong, it can become right faster.
Doing the dishes? Back up home.
Mowing the lawn? Back up root.
Working AFK or socializing? Back up effects.