ALLOW_SSH_ROOT_USER only looks in main sshd_config, add sshd_config.d
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dogsbody,
dogsbodymark
bookworm (I'm sure other distros as well) added /etc/ssh/sshd_config.d for user changes making package updates easier and cleaner. Sadly when PermitRootLogin is set in a sub config rkhunter doesn't look follow to find it and falsely reports it.
Maybe a way could be added to parse the sshd_config file to find includes?
It's actually a security issue since someone can add PermitRootLogin in /etc/ssh/sshd_config and then override it in /etc/ssh/sshd_config.d/ later on.