I'm far from an expert, or even a semi-amateur with computer design, but I think Hillis is arguing that physical realities/constraints should deeply influence the theoretical computational process itself, regardless of implementation details. I don't see this as tainting or complicating the pure, theoretical aspects of Computer Science with messy implementation details that are going to change in 2 years anyway (presumably, hard realities observed through Physics will stick around for a long, long time, until/unless we discover them to be different). Rather, I see this as another place where we can use Nature as a design guide.