f.lux does take some getting used to. However you can adjust it to suit your own idea of what a comfortable color shift is for nighttime. I've been using it happily for years. Now that Sierra has it's own night shift I guess I'll get around to trying it eventually. But the Apple version, as usual, cannot be customized. As is usual with Apple, it's a take it or leave it proposition, when you have any choice at all, which you often do not. At least with NightShift you can ignore it.
The only drawback to f.lux I've found is that it's a bit difficult to understand how to set the parameters. I don't get the point of the bedtime settings.