This is a fresh install, and Akonadi won't start with

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QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root'
mysqld: [ERROR] Could not open required defaults file: /etc/xdg/akonadi/mysql-global.conf
mysqld: [ERROR] Fatal error in defaults handling. Program aborted!
org.kde.pim.akonadiserver: database server stopped unexpectedly
org.kde.pim.akonadiserver: Database process exited unexpectedly during initial connection!
org.kde.pim.akonadiserver: executable: "/usr/sbin/mysqld-akonadi"
org.kde.pim.akonadiserver: arguments: ("--defaults-file=/root/.local/share/akonadi/mysql.conf", "--datadir=/root/.local/share/akonadi/db_data/", "--socket=/tmp/akonadi-root.YwZ8QB/mysql.socket", "--pid-file=/tmp/akonadi-root.YwZ8QB/mysql.pid")
org.kde.pim.akonadiserver: stdout: ""
org.kde.pim.akonadiserver: stderr: "2018-12-01T11:39:36.018991Z 0 [Warning] The syntax '--log_warnings/-W' is deprecated and will be removed in a future release. Please use '--log_error_verbosity' instead.\n2018-12-01T11:39:36.019037Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).\n2018-12-01T11:39:36.019045Z 0 [Warning] 'NO_AUTO_CREATE_USER' sql mode was not set.\n2018-12-01T11:39:36.019070Z 0 [Warning] Insecure configuration for --secure-file-priv: Current value does not restrict location of generated files. Consider setting it to a valid, non-empty path.\n2018-12-01T11:39:36.019091Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.24-0ubuntu0.18.04.1) starting as process 21287 ...\n2018-12-01T11:39:36.021368Z 0 [ERROR] Fatal error: Please read \"Security\" section of the manual to find out how to run mysqld as root!\n\n2018-12-01T11:39:36.021395Z 0 [ERROR] Aborting\n\n2018-12-01T11:39:36.021425Z 0 [Note] Binlog end\n2018-12-01T11:39:36.021501Z 0 [Note] /usr/sbin/mysqld: Shutdown complete\n\n"
org.kde.pim.akonadiserver: exit code: 1
org.kde.pim.akonadiserver: process error: "Unknown error"
org.kde.pim.akonadiserver: Failed to remove runtime connection config file
org.kde.pim.akonadicontrol: Application 'akonadiserver' exited normally...

All the files exist and are readable by root. I tried starting mysqld manually, but it complains that the user "mysql" does not exist. I tried creating one, but it doesn't work. I also tried the most common "solution" to this problem which is deleting /var/lib/mysql and /var/lib/mysql-files and recreating them, but it doesn't help.

I already tried wiping akonadi/mysql/kontact/kmail and etc and re-installing to no avail.

You should never run Akonadi (or even the entire KDE session) as root, only as a regular user.

In this case, MySQL will not start under the root user for security reasons, you will probably need to add some special configuration to ~/.config/akonadi/akonadiserverrc that will override this behavior in MySQL, but I strongly recommend against it.