I think it's a balancing act. One the one hand, our bodies adapt to make the best of the dietary choices available, though I question the time-scale that is needed to make any of those adaptations inheritable. But on the other hand, there's nothing that says that the choices available to our ancestors, despite whatever adaptations they may have made, were necessarily optimal.

So I would tend to come at it from a slightly different perspective. Yes, our genes go a long way in dictating the kind of nutrition we need for optimal health. To the degree that our ancestors shared those genes (and given how interbred most of us have become, that's not necessarily a good assumption) it is reasonable to assume that they adopted diets that met those needs about as well as possible given the range of options available to them. It's actually unlikely that those options allowed them to devise a truly optimal diet for their genetic make-up, but the choices they settled on provide good clues as to what might be important for us.