Did you ever dig in to see why that changed? I'm surprised that in a steady-state (not booting or restarting services) systemd/not-systemd would have an impact.
Should these issues be fixed by CPU/IO schedulers? Are there any systemd realtime tasks involved?
Or is the fact that systemd is the one doing it that much worse? Does systemd-timesyncd take more time than chronyd launched by some other init? I'd be surprised.