But apparently I'm some bastard n00b that does not care about security enough! Can you imagine trying to access your files from your editor like you've been doing for decades? This guy doesn't get it!
Apparently flatpak et al have the same problems.
In my case, I'm not sure where to switch. I want easy of use, I don't really enjoy meddling with the OS. I use Xubuntu because it works better out of the box for me, but if I have to deal with this, I'm not interested.
Then for apps that have dotfile-type directories where you can put config files and other stuff, those simply exist in app-specific directories under .var in your home directory, so they're not difficult to find either.
Unfortunately that still breaks any kind of multi-file format, where opening one file might implicitly require accessing additional other files, and in some cases those additional files might even be distributed all over the directory hierarchy.