Arch system for reference. The latest version of system 241.93 has implemented a change to PID files being stored in subdirectories below /var/run - from my dmesg:
[173100.352314] systemd[1]: /usr/lib/systemd/system/chronyd.service:9: PIDFile= references path below legacy directory /var/run/, updating /var/run/chrony/chronyd.pid → /run/chrony/chronyd.pid; please update the unit file accordingly.