Of course it tracks what time each server is serving (and other meta data). That's how the system knows that many servers didn't advertise the leap second when

Of course it tracks what time each server is serving (and other meta data). That's how the system knows that many servers didn't advertise the leap second when they should have (at which time it's too late for the NTP Pool to do anything useful about it). Reportedly several national time sources (not NIST) managed to not announce the leap second, too.