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> [...] gdm3 thinks that there are zero user accounts and it launches gnome-initial-setup.

What if the root user intentionally deleted all non-root users? GDM would just let anyone creates an user with wheel?

The root user obviously counts as a user account, otherwise you would be prompted to make a new account on every startup if you hadn't made any other accounts. The reason why it thinks there are zero accounts in this instance is because you've just killed the service daemon that would provide that number, so no number is received through the DBus call.

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