Promising so far. Just received the replacement iPhone X today. I’ve been able to use the phone thus far without throbbing pain, but it hasn’t been an hour yet. There is some color variance between the replacement and the iPhone X I’ve been using (the replacement is warmer even without True Tone off on both which I prefer anyway). I did pickup my first X and experienced some strain almost immediately. Wouldn’t be surprised if the eye pain creeps back but seems better so far.
It is extremely unlikely that there's any difference in the actual PWM algorithm between two units; The PWM frequency and amplitude used for any given screen brightness are core parts of the display driving and will not vary between units.
On the other hand, it is possible is that the actual degree of PWM dimming used at a given "true" (visible) brightness could change if a screen has a different peak light output -- For example, a screen that is 20% dimmer at full output doesn't need to use as much PWM dimming to reach the same light output as a brighter panel.
My other hypothesis would be that the warmer screen is less irritating to the eye in general, especially in those PWM output spikes, and that might be just enough reduction in discomfort to make it usable for you. Either way I hope it works for you.
BTW, if you still have the old phone it'd be interesting to know if there's a difference between how bright they can get when manually set to 100%. Might be hard to tell with the different white points though.