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ntpd can be configured to disallow negative time adjustments, and anything that runs a database definitely should have that configured. The system clock is presumed to always increment for most databases, and screwing with that can cause data loss.

I think the concern is more about whether the negative leap second handling in all of the different, interacting NTP server implementations (which have never been exercised in the wild) will be good, bad or ugly.

If you read around the topic, there was plenty of non-conformance for the relatively recent leap seconds.

As you say, clock skewing happens continuously in NTP so that part looks proven.

What about my DIY double entry book system I wrote using various JavaScript libraries?

I have no clue.