Aqui está um trecho desse post:
/run/user/$uid is created by pam_systemd and used for storing files used by running processes for that user. These might be things such as your keyring daemon, pulseaudio, etc.
Prior to systemd, these applications typically stored their files in /tmp. They couldn't use a location in /home/$user as home directories are often mounted over network filesystems, and these files should not be shared among hosts. /tmp was the only location specified by the FHS which is local, and writable by all users.
So systemd came along and created /run/user/$uid. This directory is local to the system and only accessible by the target user.
Para resolver sua preocupação, isso não deve ser um problema, a menos que os usuários estejam consumindo muito espaço em / tmp, o que é realmente uma memória com suporte a permuta. Obrigado a Patrick por essa ótima resposta.