I suspect Ubi just didn't get enough time to optimize against the S.Ironically Micrososft calling it a 1440p machine is probably what led to Ubisoft going for 1440p on Valhalla...
Most people won't be able to tell the difference between the two devices, even with 30 vs 60 fps in an action game like AC. Especially if they're not swapping back and forth between the two. It doesn't feel bad, it doesn't look bad. There's no intuitive reference point for the difference.
We've already hit diminishing returns pretty hard on graphics quality, and I think people in communities like these underestimate how hard it is for "normal" people to recognize the kinds of graphical differences that'll exist between the X and S.
The AC Valhalla fps gap is more of a pr issue than something the vast majority of the user base is going to notice the effects of.