This doesn't agree with my experience. If the time were consistently off by multiple seconds then the sweep second hand on my apple watch would stutter whenever the time was re-synchronized, but it does not.
In general though, you need to look in more detail at what your exact configuration is and find out what you have misconfigured.
Having to set registry values to get sane syncing behavior is just nuts when, again, my cheap Casio watch - which possesses a miniscule fraction of the features of a modern computing device - can deliver sub 500ms accuracy with absolutely zero fuss.