I tried another time and this time I waited longer. I see the following time gap in the logs of this reboot process:
Apr 26 01:57:33 systemd[1]: firewalld.service: Deactivated successfully.
Apr 26 01:57:33 systemd[1]: Stopped firewalld.service - firewalld - dynamic firewall daemon.
Apr 26 01:57:33 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=firewalld comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 01:57:33 systemd[1]: Stopping polkit.service - Authorization Manager...
Apr 26 01:57:33 systemd[1]: polkit.service: Deactivated successfully.
Apr 26 01:57:33 systemd[1]: Stopped polkit.service - Authorization Manager.
Apr 26 01:57:33 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=polkit comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 01:57:33 audit: BPF prog-id=70 op=UNLOAD
Apr 26 01:57:33 audit: BPF prog-id=60 op=UNLOAD
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Metadata removal from repository cache in path "/var/cache/dnf5daemon-server/terra-2cbdb71aadff9295" complete. Removed 5 files, 1 directories (total of 731040 bytes). 0 errors
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Solv files removal from repository cache in path "/var/cache/dnf5daemon-server/terra-2cbdb71aadff9295" complete. Removed 2 files, 1 directories (total of 803588 bytes). 0 errors
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] DEBUG Downloading metadata for repo "terra"
Apr 26 02:02:03 dnf5daemon-server[2401]: 2025-04-25T23:02:03+0000 [2401] TRACE countme: no event for repo "terra": window already counted
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] WARNING Error loading repo "terra" (skipping due to "skip_if_unavailable=true"):
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] WARNING std::exception
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "@System" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "copr:copr.fedorainfracloud.org:dsommers:openvpn3" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "fedora" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "@System" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "fedora-cisco-openh264" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-free" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-free-updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-nonfree-updates" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "rpmfusion-nonfree" with added file provides
Apr 26 02:02:05 dnf5daemon-server[2401]: 2025-04-25T23:02:05+0000 [2401] DEBUG Rewriting repo "code" with added file provides
Apr 26 02:02:05 systemd[1]: dnf5daemon-server.service: Deactivated successfully.
Apr 26 02:02:05 systemd[1]: Stopped dnf5daemon-server.service - DNF daemon.
Apr 26 02:02:05 systemd[1]: dnf5daemon-server.service: Consumed 1.041s CPU time, 323.4M memory peak.
Apr 26 02:02:05 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:init_t:s0 msg='unit=dnf5daemon-server comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=? terminal=? res=success'
Apr 26 02:02:05 systemd[1]: Stopped target basic.target - Basic System.
The time gap is between Apr 26 01:57:33 and Apr 26 02:02:03 when dnf5daemon-server started to log something related repositories sync during the reboot.
Could the following be also related to this issue fix of which was adopted by the dnfdragora package maintainer?
Will try restarting Fedora when dnfdragora-updater is not running.