Ultimately I have modified the etc/syslog-ng.conf with:
destination messages {
file("/var/log/messages" suppress(5) template("${R_YEAR}-${R_MONTH}-${R_DAY} ${R_HOUR}:${R_MIN}:${R_SEC} ${PRIORITY} ${PROGRAM}[${PID}]: ${MSGONLY}\n") log_fifo_size(256));
};
Afterwards the output timestamps in system log are aligned (but apparently this is not solving the root cause of the issue, only the output formatting).
And probably needs to be manually re-applied after each update.
Solution found in this topic: Time difference is System log