The problem with "seconds since the Epoch" is that if you naively add milliseconds, it is no longer monotonic.
Since 2016-12-31T23:59:60Z is 1483228800 seconds since the Epoch, and 2017-01-01T00:00:00Z is also 1483228800 seconds since the Epoch, that means that 2016-12-21T23:59:60.xxxZ would have the same timestamp as 2017-01-01T00:00:00.xxxZ, for all xxx.
This corresponds to the counter jumping backward 1000 milliseconds at 2017-01-01T00:00:00.000Z.
Since 2016-12-31T23:59:60Z is 1483228800 seconds since the Epoch, and 2017-01-01T00:00:00Z is also 1483228800 seconds since the Epoch, that means that 2016-12-21T23:59:60.xxxZ would have the same timestamp as 2017-01-01T00:00:00.xxxZ, for all xxx.
This corresponds to the counter jumping backward 1000 milliseconds at 2017-01-01T00:00:00.000Z.