Ah, I see what was going on.
We use chrony instead of ntp for better programibility, and if you install ntp it removes both chrony and the packages that depend on it (like magni_bringup).
For time syncing with chrony:
On the laptop (with chrony installed):
sudo chronyc -a local stratum 10
sudo chronyc -a allow 0/0
On the pi (with chrony installed):
sudo systemctl stop magni-base
sudo chronyc -a add server LAPTOP iburst
sudo chronyc -a burst 2/4
sudo systemctl start magni-base