Huge thanks to @worldofpeace and @jtojnar for all their help on IRC.
The users were being skipped by accountsservice because the shells were set to an entry outside of those listed in /etc/shells (see here for what happens).
/var/run has been deprecated (in favour of /run) but not removed from my 19.03 config when pushing to a new 19.09 machine. Recommendation to instead use users.defaultUserShell = pkgs.<preferred-shell> instead of strings containing paths and so my config now does this!