First and foremost, you are outright dismissing Flatpak, which accomplishes all of your goals pretty much, with a vague desire to use “plain old Linux” instead of a proper motivation. You should really stop and ask yourself, WHY not Flatpak? What do you actually want, and why is Flatpak not the answer to that?

I point this out first because then in the next paragraph you mention some tools such as Firejail. Which is attempting to do more or less the same as flatpak, but in a more crude/less polished form. And neither Flatpak or Firejail are “plain linux”, they’re just fancy wrappers around a whole bunch of actual “Linux features”, like namespaces, seccomp, cgroups, users, chroot, filesystem permissions, and other higher-level tools such as bubblewrap (in the case of flatpak).

So, do you want to learn the underlying primitives/underlying tooling? If so, start with users, filesystem permissions, and Linux namespaces and the other Linux features I’ve listed.

Or do you want to just deploy applications in a sandboxed environment? If so, use Flatpak/Firejail/Snap/Linux containers such as Podman or Docker, etc. Then manage permissions using Flatseal (in the case of flatpak), and you’re done.

How should I do this? I need some sources to read all about linux user accounts.

You should stick with trusted sources such as TLDP, Redhat/Fedora docs, Archlinux Wiki, Gentoo Wiki, etc. For example, regarding users:

• https://tldp.org/LDP/GNU-Linux-Tools-Summary/html/c6239.htm
• https://docs.redhat.com/en/documentation/red_hat_enterprise_linux/7/html/system_administrators_guide/ch-managing_users_and_groups#s2-users-tools-groups-add
• https://wiki.archlinux.org/title/Users_and_groups

AFAIK signal stil requires a phone numer for registration, however you now can add people by their username.

E-mail is horrible for privacy, spam, instant messaging, etc. PGP “works” in very limited scenarios, and e-mail is not really one of them.

Plus these two statements seem unplausible for me:

we can assume you’re protected by PGP when writing to most users,

and

and with the added effect of not needing to convince anyone to install anything since from their end it’s just an email.

I disagree with the first statement, most users don’t know what PGP is and therefore don’t have keys, so you can’t encrypt anything to them. The only way most users would use PGP is if something sets it up for them, alá protonmail or my using some special client. Since you’ve said that from their end it is just an e-mail, how does Deltachat add any meaningful encryption?