In the latest upstream code all important changes made by chronyc should be now logged, e.g. added/removed sources (including changes in sourcefiles) and access restrictions, reloaded keys, modified makestep, etc. To avoid spamming the log with unnecessary information it doesn't log commands that don't change anything important for chronyd operation (e.g. dumping sources) or already have a related log message (e.g. adding or removing a manual sample triggers the "making a frequency change/slew" message).
This issue will be fixed by rebase to chrony-4.4 (bug #2231078).